Before the 2000 season, Dave Wannstedt, formerly of the Chicago Bears, became the new coach, and ex-Jacksonville Jaguars backup Jay Fiedlerbecame the new quarterback, even though former Marino backup Damon Huard had been considered the favorite. Despite lowered expectations, the defense broke through with Jason Taylor and Trace Armstrong each getting 10 sacks, and four players (Sam Madison, Brian Walker, Brock Marionand Patrick Surtain) tallying at least five interceptions. All-pro linebacker Zach Thomas also contributed many tackles. In addition, Lamar Smithrushed for 1,139 yards, and Miami finished atop the AFC East with an 11–5 record. In the first round of the playoffs, Miami took the Indianapolis Coltsto overtime and won on a Lamar Smith touchdown run. Smith finished with 209 yards on 40 carries, but in the next round, the Dolphins were shut out by the Oakland Raiders, and a worn-out Smith was barely able to run. The 2001 offseason brought in rookie Chris Chambers at wide receiver, but Trace Armstrong left, as did two offensive linemen, Richmond Webb, a Pro Bowl anchor since 1990, and Kevin Donnalley. During the 2001 season, the Dolphins relied on a strong defense to finish 11–5, earning a Wild Card spot and finishing second in the AFC East behind the eventual Super Bowl champions, the New England Patriots. The Dolphins lost in the first round of the playoffs 20–3 to the Baltimore Ravens.
Miami revitalized its running game in time for the 2002 season by trading for New Orleans Saints running back Ricky Williams. In addition, rookie tight end Randy McMichael made his presence felt. The Dolphins replaced Chan Gailey as offensive coordinator, and behind a new scheme under Norv Turner and a power running game led by Williams, Miami quickly rushed out to a 5–1 start, highlighted by the Dolphins' first victory over the New York Jets since 1997 and an incredible last minute comeback by Fiedler against the Broncos. However, Fiedler injured his thumb and missed the next six games. This intrigued some Dolphins fans, who believed backup Ray Lucas could outdo the much-maligned Fiedler, a view based in part on Lucas' 6–3 record with the 1999 Jets. However, Lucas was abysmal in losses to the Bills and Packers and merely average in a 13–10 loss to the Jets. Miami rebounded with wins over Baltimore and an impressive thumping of San Diego, but were crushed 38–21 in a snowstorm at Buffalo; Lucas was benched and Fiedler made his return to the team. Still, Miami pulled off an impressive win over the Oakland Raiders and sat at 9–5 with two weeks left in the season, in prime position to steal the AFC East. However they were beaten by the Vikings and then in Week 17 blew an 11-point lead late in the fourth quarter of a devastating loss to the Patriots. Due to a tiebreaker, both the Dolphins and Patriots lost out on the playoffs as the Jets took the AFC East title. Many fans called for Wannstedt's firing, but he was kept on for the 2003 season. Despite it all, the team believed it had plenty to look forward to, as Ricky Williams broke team records with 1,853 rushing yards and 16 touchdowns on the ground.
The Dolphins began the 2003 season with a 21–20 loss to the Houston Texans, but they rebounded to win four straight games. During a crushing overtime loss at the hands of the Patriots, Jay Fiedler was injured, forcing newly acquired backup Brian Griese to lead the Dolphins to victory the next week over San Diego. That, however, was Griese's high point, and after a good showing against Indianapolis in a losing effort (he threw for 231 yards and a touchdown in the 23–17 Colts win), he struggled against the Titans, throwing three interceptions in a 31–7 Tennessee win, and was highly ineffective against the Ravens, managing just 126 yards in a 9–6 overtime win. The Dolphins fell behind to theWashington Redskins after Griese threw two interceptions; trailing 20–7, Fiedler came off the bench and led a comeback victory, 24–23. Miami looked like it might rebound thanks to a 40–21 Thanksgiving Day victory over the Dallas Cowboys that took them to 8–4, but two key losses to the Patriots and the Eagles ended Miami's postseason hopes. Miami finished 10–6 after victories over Buffalo and the Jets.
The 2004 offseason was disastrous for Miami. Tight end Randy McMichael was arrested for domestic violence and wide receiver David Boston (signed from San Diego) suffered an injury in training camp and missed the entire season (Boston also failed a drug test for steroids later in the season). But the biggest shock came when Ricky Williams retired for then-unspecified reasons. Eventually it was revealed that a) Williams had recently incurred his third strike under the NFL's substance abuse policy, and b) to a lesser degree felt he was unnecessarily overused by Wannstedt. Many experts predicted a disastrous season for the Dolphins. These predictions proved right as Miami dropped its first six games of the 2004 season, marking the worst start in franchise history at the time. The team fell to 1–8, leading Wannstedt to resign on November 9. He was replaced on an interim basis by defensive coordinator Jim Bates. The Dolphins fared slightly better under Bates, winning three of their final seven games, including a 29–28 upset victory over the defending champion Patriots. Despite this, the Dolphins decided not to hire Bates for the permanent coaching position.
The Dolphins hired LSU coach Nick Saban. With the second pick in the 2005 NFL Draft, Nick Saban elected to go with Auburn running back Ronnie Brown. The Dolphins struggled, losing seven of their first ten games to fall to 3–7. After a frustrating two months, however, the Dolphins rallied, winning their final six games, including a win to end the season over the New England Patriots. The team finished 9–7, missing the playoffs. In the offseason the Dolphins showed major interest in signing free agent quarterback Drew Brees; however, Miami was unsure if Brees' shoulder was completely healed from a labrum tear he suffered with the San Diego Chargers . The Dolphins ended negotiations and traded for Minnesota Vikings QB Daunte Culpepper instead, a move that would haunt Miami Dolphins fans to this day.
In Saban's second season, the Dolphins were expected to contend for a playoff spot. The season, however, turned out to be a major disappointment. Culpepper never recovered from the devastating knee injury he suffered in 2005, was benched after the fourth game of the season and eventually put on injured reserve. After starting the season 1–6, the Dolphins won four straight and were back in the playoff hunt at 5–6, but a few losses later ended their playoff hopes. This was Saban's first and last losing season as a head coach of the Miami Dolphins. On January 3, 2007, Saban announced that he had accepted a contract for eight years and a guaranteed $32 million to coach at the University of Alabama. Saban left despite making several public statements in the preceding weeks assuring fans and owner Wayne Huizenga that he would be staying on as coach.
Cam Cameron, previously the offensive coordinator for the Chargers, was hired as the new head coach. The Dolphins finished the 2007 season with a 1–15 record, the worst in franchise history. Late in the season, two-time Super Bowl winning coach Bill Parcells was named Executive Vice President of the Dolphins football operations. Shortly after the season finale, Parcells fired general manager Randy Mueller and on January 3, 2008, head coach Cam Cameron was fired along with almost all of his staff. That same offseason, the Dolphins also parted ways with two long-time Dolphins, releasing linebacker Zach Thomas (who later signed with the Dallas Cowboys) and trading defensive endJason Taylor to the Washington Redskins for a second round draft pick.
Parcells then hired Tony Sparano, who was previously an assistant under Parcells during his days as the head coach of the Dallas Cowboys. The Dolphins took Jake Long, star offensive lineman out of the University of Michigan with the first pick of the 2008 draft and drafted quarterback Chad Henne with their second round pick (the second consecutive year they drafted a QB in the second round). After the New York Jets traded for Brett Favre and released quarterback Chad Pennington the same day, the Dolphins quickly signed Pennington, who was a former Parcells draft pick. After starting the 2008 season with a 0–2 record the Dolphins used the "wildcat" offense against the New England Patriots on six plays, which produced four touchdowns (three rushing and one passing) in a 38–13 upset victory. The wildcat offense or single-wing was a "new" formation that allowed the Dolphins to utilize their two best offensive players, Ronnie Brown and Ricky Williams, both of which played the same position. From that point on the Dolphins completed the greatest single-season turnaround in NFL history, going from a 1–15 in 2007 to 11–5. Additionally, Miami won the AFC East, becoming the first team in NFL history to win their division after only having one win the previous season. However, the Dolphins lost in the first round of the playoffs to the Baltimore Ravens, 27–9.
In 2009 the Dolphins again started off 0–2. In week 3 Chad Pennington suffered a shoulder injury against the San Diego Chargers and was out for the rest of the 2009 season. Second year quarterback Chad Henne replaced him. Under Henne, the Dolphins won their first two games before losing to the Saints after leading 24–3 towards the end of the first half. The Dolphins finished the rest of the season without Ronnie Brown, who was sidelined by a Lisfranc foot injury that required surgery. Ricky Williams was the starter again and finished the season with 1,121 yards, beating his own rookie year at the age of 32. Miami ended the season with three consecutive losses to finish 7–9 and out of the playoffs. The Dolphins looked to bounce back the next season by acquiring Brandon Marshall from the Denver Broncos for two second-round draft picks, and Karlos Dansby via free agency. Ronnie Brown was back from his leg injury the previous year, and Ricky Williams also returned (while many speculated he would retire). During the 2010 NFL Draft, the Dolphins selected Jared Odrick with their first-round draft pick. In September 2010, Bill Parcells, stepped down as Vice President of Football Operations, but remained as a consultant. He was later criticised for not making the right choices to improve the team. The Dolphins started out 2010 by winning their first two games against the Buffalo Bills and the Minnesota Vikings (at Buffalo and Minnesota, respectively). However the rest of the Dolphins season would be a disappointment. They finished the season with another 7–9 again, missing the playoffs for the 8th time in 9 years. Questions were raised about Chad Henne and Coach Sparano's futures with the team. It was reported that Stephen Ross was interested in hiring Stanford head coach Jim Harbaugh after flying to California to meet him; however, Ross denied those rumors, and in that same week he gave Tony Sparano a three-year extension.
With their first pick in the 2011 NFL Draft, and 15th selection overall, the Dolphins selected center Mike Pouncey from Florida, and with their second pick, running back Daniel Thomas. The Dolphins also acquired Reggie Bush from the New Orleans Saints in a trade. Miami then cut Channing Crowder and added Kevin Burnett to replace him. Jason Taylor re-signs for his third stint. The Dolphins got off to a disastrous 0-7 start, rebounded to win four of the next five games, and then lost 26–10 to the struggling Philadelphia Eagles, effectively ending their chance at playoff contention and Tony Sparano's job as Head Coach. Todd Bowles stepped in as interim coach. The Dolphins won two of their final three games, including a win over the Jets that that ended the Jets' playoff chances in Jason Taylor's final NFL game.
The Dolphins, looking to move on from the Tony Sparano era, hired former Green Bay Packers offensive coordinator Joe Philbin on January 20, 2012, to serve as their tenth head coach. Philbin had served as the Packers OC for five years, during which time their offense was never ranked below tenth in the NFL. In the offseason, fans organized a protest outside the Dolphins' team facility to call for the firing of General Manager Jeff Ireland. The Dolphins were in contention to hire former NFL head coach Jeff Fisher, but he accepted the head coach position with the St. Louis Rams and the Dolphins hired Philbin instead. The Dolphins also pursued quarterbacks Peyton Manning, Matt Flynn andAlex Smith, all of whom chose to sign elsewhere. The Dolphins signed David Garrard and selected Ryan Tannehill with the 8th pick in the 2012 NFL Draft.
Garrard originally won the starting QB battle against Tannehill and Moore in training camp, but injured his knee in a bizarre accident at home. Rookie Ryan Tannehill won the starting job for the 2012 season after a strong showing in preseason and camp. Garrard was eventually released.
In his first game as a professional football player, Tannehill struggled, throwing three interceptions in a loss on the road against the Houston Texans. His first home game was a much different story, as he ran for a touchdown and did not commit any turnovers while dominating the Oakland Raiders. Miami then lost back-to-back OT games against the Jets and the Arizona Cardinals, despite Tannehill throwing for 431 yards, the most ever for a rookie QB in a single game in team history, and Brian Hartline racking up 253 receiving yards, the most ever by a Dolphin receiver, in the game against Arizona. Now facing questions about finishing games, they played Cincinnati on the road and won 17–13 win after Reshad Jones picked off the ball with under a minute and a half left in the game. Despite an impressive 4–3 start a potential AFC Wildcard spot, the Dolphins lost a highly touted game against the Colts, 23–20. This started a 3-game losing streak, raising many questions about the team. After staying in Wild Card contention through Week 16, Miami finished 7–9 after being shutout by the Patriots.
With many question marks about the future of some popular players, including Jake Long, the Dolphins went into the off season looking for help at many positions. They started off free agency by re-signing Brian Hartline, and added Mike Wallace, Dannell Ellerbe, Phillip Wheeler, Dustin Keller, and Brandon Gibson, but losing Long and Sean Smith.
After the signings of Brandon Albert, Cortland Finnegan, Louis Delmas, and Earl Mitchell and a break out season for Jelani Jenkins. The Miami Dolphins finished 8-8 after a good run almost making the playoffs if not for a losing streak near the end of the season.