- New York Mets selected Carlos Mendoza in free agent draft on November 18, 1997.
- New York Mets claimed David Lamb on waivers from the Tampa Bay Devil Rays on February 7, 2000.
- New York Mets traded Paul Wilson and Jason Tyner to the Tampa Bay Devil Rays for Rick White and Bubba Trammell on July 28, 2000.
- Tampa Bay Devil Rays claimed Brian Rose of the New York Mets on waivers on April 24, 2001.
- Tampa Bay Devil Rays signed Tom Martin of the New York Mets as a free agent on January 28, 2002.
- New York Mets traded Rey Ordonez to the Tampa Bay Devil Rays for Russ Johnson and Josh Pressley on December 15, 2002.
- New York Mets signed free agent Dan Wheeler of the Tampa Bay Devil Rays on January 27, 2003.
- New York Mets traded Scott Kazmir and Joselo Diaz to the Tampa Bay Devil Rays for Victor Zambrano and Bartolome Fortunato on July 30, 2004.
- Tampa Bay Devil Rays signed Jason Roach of the New York Mets as a free agent on November 22, 2004.
- Tampa Bay Devil Rays signed Brian Buchanan of the New York Mets as a free agent on December 17, 2004.
- New York Mets purchased Brian Stokes from the Tampa Bay Devil Rays on November 28, 2007.
- Tampa Bay Rays signed Mike DiFelice of the New York Mets as a free agent on January 6, 2008.
- Tampa Bay Rays signed Chris Carter of the New York Mets as a free agent on January 7, 2011.
- New York Mets signed free agent Dale Thayer of the Tampa Bay Rays on February 6, 2011.
- New York Mets signed free agent Asdrubal Cabrera of the Tampa Bay Rays on December 9, 2015.
- New York Mets traded Lucas Duda to the Tampa Bay Rays for Drew Smith on July 27, 2017.
- New York Mets signed free agent Carlos Gomez of the Tampa Bay Rays on March 7, 2019.
- New York Mets traded Neraldo Catalina to the Tampa Bay Rays for Wilmer Font on May 6, 2019.
- Tampa Bay Rays signed Brooks Pounders of the New York Mets as a free agent on February 15, 2020.
- Tampa Bay Rays signed Michael Wacha of the New York Mets as a free agent on December 18, 2020.
- New York Mets signed free agent Aaron Loup of the Tampa Bay Rays on January 30, 2021.
- Tampa Bay Rays signed Hunter Strickland of the New York Mets as a free agent on February 2, 2021.
- New York Mets traded Tommy Hunter and Matt Dyer to the Tampa Bay Rays for Rich Hill on July 23, 2021.
- New York Mets claimed Jake Reed on waivers from the Tampa Bay Rays on August 2, 2021.
- New York Mets traded Keyshawn Askew to the Tampa Bay Rays for Brooks Raley on December 7, 2022.
- New York Mets purchased Phil Maton from the Tampa Bay Rays on July 9, 2024.
- New York Mets traded to the for on .
- New York Mets traded Eric Orze to the Tampa Bay Rays for Jose Siri on November 19, 2024.
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