- New York Mets claimed Yoan Lopez on waivers from the on 9, 0220.
- New York Mets selected Chris Donnels in free agent draft on November 17, 1992.
- Florida Marlins signed Dave Magadan of the New York Mets as a free agent on December 8, 1992.
- New York Mets traded Steve Long to the Florida Marlins for Robert Person on March 30, 1994.
- New York Mets traded Quilvio Veras to the Florida Marlins for Carl Everett on November 29, 1994.
- Florida Marlins signed Joe Orsulak of the New York Mets as a free agent on December 5, 1995.
- Florida Marlins signed Brian Daubach of the New York Mets as a free agent on November 7, 1996.
- New York Mets traded Fletcher Bates and Scott Comer to the Florida Marlins for Dennis Cook on December 18, 1997.
- New York Mets traded A.J. Burnett, Jesus Sanchez and Robert Stratton to the Florida Marlins for Al Leiter and Ralph Milliard on February 6, 1998.
- New York Mets traded Preston Wilson, Geoff Goetz and Ed Yarnall to the Florida Marlins for Mike Piazza on May 22, 1998.
- New York Mets traded Jorge Fabregas to the Florida Marlins for Oscar Henriquez on November 20, 1998.
- New York Mets signed free agent Dennis Springer of the Florida Marlins on February 4, 2000.
- Florida Marlins signed Ryan McGuire of the New York Mets as a free agent on November 3, 2000.
- New York Mets signed free agent Braden Looper of the Florida Marlins on January 6, 2004.
- Florida Marlins signed Al Leiter of the New York Mets as a free agent on December 8, 2004.
- Florida Marlins signed Wilson Delgado of the New York Mets as a free agent on December 16, 2004.
- New York Mets signed free agent Ramon Castro of the Florida Marlins on December 22, 2004.
- New York Mets traded Mike Jacobs, Yusmeiro Petit and Grant Psomas to the Florida Marlins for Carlos Delgado on November 24, 2005.
- New York Mets traded Gaby Hernandez and Dante Brinkley to the Florida Marlins for Paul Lo Duca on December 5, 2005.
- New York Mets traded Henry Owens and Matt Lindstrom to the Florida Marlins for Jason Vargas and Adam Bostick on November 20, 2006.
- Florida Marlins signed Jeff Conine of the New York Mets as a free agent on March 28, 2008.
- Florida Marlins signed Willie Collazo of the New York Mets as a free agent on November 25, 2008.
- New York Mets signed free agent Ronny Paulino of the Florida Marlins on December 7, 2010.
- New York Mets signed free agent Vinny Rottino of the Florida Marlins on November 16, 2011.
- Florida Marlins signed Jose Reyes of the New York Mets as a free agent on December 7, 2011.
- Miami Marlins signed Jon Rauch of the New York Mets as a free agent on February 5, 2013.
- Miami Marlins signed Jordany Valdespin of the New York Mets as a free agent on December 20, 2013.
- Miami Marlins signed Zach Lutz of the New York Mets as a free agent on January 21, 2016.
- New York Mets traded Ricardo Cespedes and Merandy Gonzalez to the Miami Marlins for A.J. Ramos on July 28, 2017.
- Miami Marlins signed Eric Campbell of the New York Mets as a free agent on February 17, 2018.
- New York Mets claimed Stephen Tarpley on waivers from the Miami Marlins on January 8, 2021.
- New York Mets traded Federico Polanco to the Miami Marlins for Jordan Yamamoto on February 1, 2021.
- New York Mets traded David Robertson to the Miami Marlins for Marco Vargas and Ronald Hernandez on July 27, 2023.
- New York Mets traded Wilfredo Lara to the Miami Marlins for Huascar Brazoban on July 30, 2024.
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