The deadline for teams to use the franchise tag was 4 p.m. ET.
The team's decision means that left tackle Jake Long and receiver Brian Hartline will become unrestricted free agents on March 12 unless the Dolphins can agree to contracts with both players before then.
Starks will be guaranteed $8.45 million this season if he signs the franchise tender and plays this season under that designation, a big raise from the $3.72 million he earned in 2012.
The 29-year-old Starks made the Pro Bowl as an alternate and is one of the anchors of Miami's stout run defense. He was hard to move in the middle and showed enough athleticism to also register 4.5 sacks and an interception. Starks has 32.5 sacks and four interceptions in 140 career games.
Long, the Dolphins' No. 1 overall pick in 2008, was placed on injured reserve in December because of a left triceps injury. Before that injury, the 27-year-old left tackle had missed only two games in five NFL seasons. He was chosen as a Pro Bowl starter each of the three years before 2012.
Long has become a less dominant blocker as his injuries accumulate. He was slowed by an ankle injury as a rookie and hurt his shoulder in 2010. In 2011 he battled back trouble, then missed the final game with a torn right biceps.
The 26-year-old Hartline posted career highs in receptions (74) and yards (1,083) as he provided a go-to target for first-year quarterback Ryan Tannehill.
He has 183 receptions, 2,753 yards and six touchdown catches in 60 career games.
Information from ESPN.com AFC East blogger James Walker and The Associated Press was used in this report.