- 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, Yusmiero Petit and Grant Psomas to the Florida Marlins for Carlos Delgado on November 24, 2005.
- New York Mets traded Dante Brinkley and Gaby Hernandez 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 José 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.
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