| Year | Rnd | Ovl | Phase | Player | Drafting Team | Pos | HiLvl | Played | Src | Drafted From | SF | State | AB | 2B | 3B | HR | RBI | SB | BAVG | W | L | ERA | SV | IP | SO | GS |
| 2006 | 1 | 19 | June-Reg | Brett Sinkbeil | Florida Marlins | P | MLB | 2004-2011 | C | Missouri State University | SF | MO | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 13.50 | 0 | 2 | 1 | 0 |
| 2006 | 1 | 36 | June-Reg | Chris Coghlan | Florida Marlins | 3B | MLB | 2004-2013 | C | University of Mississippi | SF | MS | 1224 | 72 | 10 | 20 | 107 | 25 | .272 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 63 | June-Reg | Thomas Hickman | Florida Marlins | CF | A+ | 2006-2010 | H | Pepperell (Rome,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 90 | June-Reg | Torre Langley | Florida Marlins | C | AA | 2006-2011 | H | Alexander (Douglasville,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 95 | June-Reg | Scott Cousins | Florida Marlins | LF | MLB | 2004-2013 | C | University of San Francisco | SF | CA | 175 | 7 | 3 | 2 | 9 | 2 | .183 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 4 | 125 | June-Reg | Hector Correa | Florida Marlins | P | AA | 2006-2012 | H | -- | SF | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 5 | 155 | June-Reg | Chris Hatcher | Florida Marlins | C | MLB | 2004-2013 | C | University of North Carolina at Wilmington | SF | NC | 7 | 0 | 0 | 0 | 0 | 0 | .000 | 0 | 0 | 5.40 | 0 | 25 | 18 | 0 |
| 2006 | 6 | 185 | June-Reg | Justin Jacobs | Florida Marlins | SS | A | 2006-2011 | H | Chino (Chino,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 7 | 215 | June-Reg | Don Czyz | Florida Marlins | P | A | 2003-2008 | C | University of Kansas | SF | KS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 8 | 245 | June-Reg | Daniel Garcia | Florida Marlins | SS | AAA | 2006-2009 | H | Nogales (La Puente,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 9 | 275 | June-Reg | John Raynor | Florida Marlins | CF | MLB | 2003-2010 | C | University of North Carolina at Wilmington | SF | NC | 10 | 0 | 0 | 0 | 0 | 0 | .200 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 10 | 305 | June-Reg | Graham Taylor | Florida Marlins | P | MLB | 2003-2012 | C | University of Miami | SF | FL | 3 | 0 | 0 | 0 | 0 | 0 | .000 | 0 | 2 | 8.18 | 0 | 11 | 5 | 3 |
| 2006 | 11 | 335 | June-Reg | Osvaldo Martinez | Florida Marlins | SS | MLB | 2006-2013 | C | Porterville College | SF | CA | 66 | 4 | 1 | 0 | 3 | 1 | .258 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 12 | 365 | June-Reg | Brad Stone | Florida Marlins | P | AAA | 2006-2011 | C | Quincy University | SF | IL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 13 | 395 | June-Reg | Drew Saylor | Florida Marlins | 2B | A- | 2003-2010 | C | Kent State University | SF | OH | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 14 | 425 | June-Reg | Jay Buente | Florida Marlins | P | MLB | 2003-2011 | C | Purdue University | SF | IN | 1 | 0 | 0 | 0 | 0 | 0 | .000 | 0 | 1 | 7.31 | 0 | 16 | 11 | 1 |
| 2006 | 15 | 455 | June-Reg | Guillermo Martinez | Florida Marlins | SS | A- | 2004-2011 | C | University of South Alabama | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 16 | 485 | June-Reg | Jake Blackwood | Florida Marlins | 3B | AA | 2006-2013 | C | Maple Woods Community College | SF | MO | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 17 | 515 | June-Reg | Hunter Mense | Florida Marlins | RF | AAA | 2004-2012 | C | University of Missouri | SF | MO | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 18 | 545 | June-Reg | Ross Liersemann | Florida Marlins | P | A+ | 2003-2007 | C | University of Akron | SF | OH | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 19 | 575 | June-Reg | Thomas Davis | Florida Marlins | P | A- | 2005-2006 | C | University of Alabama | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 20 | 605 | June-Reg | Steven Sultzbaugh ** | Florida Marlins | RF | NCAA | 2009-2010 | H | Westwood (Austin,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 21 | 635 | June-Reg | Corey Madden | Florida Marlins | P | AAA | 2005-2012 | C | St. Mary's College of California | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 22 | 665 | June-Reg | Kevan Kelley | Florida Marlins | P | RK | 2004-2006 | C | Cal State San Bernardino | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 23 | 695 | June-Reg | Rylan Hanks | Florida Marlins | P | NCAA | 2003-2003 | C | Cal State San Bernardino | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 24 | 725 | June-Reg | Ernesto Rivera | Florida Marlins | LF | - | H | Puerto Rico Baseball Acad (Gurabo,PR) | SF | PR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 25 | 755 | June-Reg | Joel Fountain | Florida Marlins | P | A | 2005-2006 | C | St. Mary's College of California | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 26 | 785 | June-Reg | Andy Jackson | Florida Marlins | P | A+ | 2006-2007 | C | University of Central Arkansas | SF | AR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 27 | 815 | June-Reg | Jeremy Hall | Florida Marlins | P | AAA | 2005-2011 | C | East Tennessee State University | SF | TN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 28 | 845 | June-Reg | Kedrick Martin | Florida Marlins | P | A- | 2007-2012 | C | Meridian Community College | SF | MS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 29 | 875 | June-Reg | Jonathan Van Looy | Florida Marlins | P | A- | 2007-2007 | H | John Swett (Crockett,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 30 | 905 | June-Reg | Quinn Harris | Florida Marlins | SS | - | H | Elizabethtown (Elizabethtown,KY) | SF | KY | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 31 | 935 | June-Reg | Willie Mays | Florida Marlins | CF | NCAA | 2008-2009 | C | Sinclair Community College | SF | OH | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 32 | 965 | June-Reg | Alejandro Sanabia | Florida Marlins | P | MLB | 2006-2013 | H | Castle Park (Chula Vista,CA) | SF | CA | 25 | 0 | 0 | 0 | 0 | 0 | .040 | 5 | 3 | 3.67 | 0 | 83 | 55 | 14 |
| 2006 | 33 | 995 | June-Reg | Eric Basurto | Florida Marlins | P | AA | 2007-2011 | C | Chabot College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 34 | 1025 | June-Reg | Thomas Kelly | Florida Marlins | P | RK | 2008-2009 | C | Bakersfield College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 35 | 1055 | June-Reg | Christopher Evans | Florida Marlins | C | - | H | Serrano (Phelan,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 36 | 1085 | June-Reg | Dave Williams | Florida Marlins | RF | MLB | 1998-2011 | C | Rutgers University | SF | NJ | 123 | 3 | 0 | 1 | 9 | 0 | .122 | 22 | 31 | 4.83 | 0 | 408 | 245 | 72 |
| 2006 | 37 | 1115 | June-Reg | James Wallace | Florida Marlins | P | - | C | College of Southern Idaho | SF | ID | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 38 | 1145 | June-Reg | Jeremie Tice ** | Florida Marlins | 3B | AA | 2008-2012 | C | Tallahassee Community College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 39 | 1175 | June-Reg | Spike McDougall | Florida Marlins | LF | AA | 2006-2009 | C | University of California-Irvine | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 40 | 1205 | June-Reg | Luis Suarez | Florida Marlins | P | RK | 2004-2006 | C | Southeastern Louisiana University | SF | LA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 42 | 1265 | June-Reg | Ryan Kussmaul | Florida Marlins | P | AAA | 2008-2013 | C | Madison Area Technical College | SF | WI | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 43 | 1294 | June-Reg | William Jackel | Florida Marlins | P | RK | 2007-2011 | C | Tallahassee Community College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 44 | 1323 | June-Reg | T.J. Forrest ** | Florida Marlins | P | Ind | 2007-2011 | H | Haughton (Haughton,LA) | SF | LA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 45 | 1352 | June-Reg | Kyle Price | Florida Marlins | 2B | NCAA | 2004-2009 | C | Eastern Oklahoma State College | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 46 | 1380 | June-Reg | Mitch MacDonald | Florida Marlins | 3B | A- | 2007-2008 | C | Monterey Peninsula College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 47 | 1408 | June-Reg | Brooks Martin | Florida Marlins | P | - | H | Streator Township (Streator,IL) | SF | IL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 48 | 1436 | June-Reg | Lance Hanmer | Florida Marlins | SS | - | H | Greensburg Community (Greensburg,IN) | SF | IN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 49 | 1464 | June-Reg | Michael Hubbard | Florida Marlins | LF | NCAA | 2008-2009 | C | University of Arkansas-Fort Smith | SF | AR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 50 | 1492 | June-Reg | Andrew Raponi | Florida Marlins | 1B | NCAA | 2007-2007 | H | Monte Vista (Danville,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |