How the current Padres got here. Idea blatantly ripped off from Will Young (no relation). More details here.
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Key:
Italics = acquired via trade.
Bold = drafted by Padres.
General manager who acquired player denoted by initials in parentheses (where no initials are provided, Kevin Towers is the GM): RS = Randy Smith, JMI = Joe McIlvaine, JMK = Jack McKeon.

Sources: Baseball Reference, Baseball Cube, Baseball America Executive Database.

Major Leagues

• Mike Adams — Free Agent (Mar 2008)
• Matt Antonelli — 1st Round (2006)
• Cha Seung Baek — Trade (May 2008)
• Jared Wells
• Josh Bard — Trade (May 2006)
  • Doug Mirabelli
    • Mark Loretta
• Michael Barrett — Trade (June 2007) [DL]
  • Rob Bowen
  • Kyler Burke
• Heath Bell — Trade (Nov 2006)
  • Ben Johnson
    • Carlos Hernandez
  • Jon Adkins
• Kevin Cameron — Rule V Draft (Dec 2006) [DL]
• Tony Clark — Free Agent (Feb 2008)
• Bryan Corey — Trade (May 2008)
• Mike Ekstrom — 12th Round (2004)
• Shawn Estes — Free Agent (Jan 2006)
• Brian Falkenborg — Waivers (Aug 2008)
• Josh Geer — 3rd Round (2005)
• Jody Gerut — Free Agent (Jan 2008)
• Brian Giles — Trade (Aug 2003)
  • Jason Bay
    • Jason Middlebrook
    • Steve Reed
  • Oliver Perez
• Adrian Gonzalez — Trade (Jan 2006)
  • Adam Eaton
    • Andy Ashby (RS)
      • Bruce Hurst (JMK)
      • Greg Harris (JMK)
  • Akinori Otsuka
  • Billy Killian
• Edgar Gonzalez — Free Agent (Nov 2007)
• Khalil Greene — 1st Round (2002) [DL]
• Scott Hairston — Trade (Jul 2007) [DL]
  • Leo Rosales
• Charlie Haeger — Waivers (Oct 2008)
• Justin Hampson — Waivers (Oct 2006)
• Chase Headley — 1st Round (2005)
• Clay Hensley — Trade (Jul 2003)
  • Matt Herges
• Trevor Hoffman — Trade (Jun 1993) (RS)
  • Gary Sheffield (JMI)
    • Jose Valentin (JMK)
    • Matt Mieske (JMK)
    • Ricky Bones (JMK)
  • Rich Rodriguez (JMK)
    • Bill Stevenson (JMK)
    • Brad Pounders (JMK)
• Nick Hundley — 2nd Round (2005)
• Kevin Kouzmanoff — Trade (Nov 2006)
  • Josh Barfield
• Wade LeBlanc — 2nd Round (2006)
• Cla Meredith — Trade (May 2006)
  • Doug Mirabelli
    • Mark Loretta
• Scott Patterson — Waivers (Oct 2008)
• Jake Peavy — 15th Round (1999)
• Mark Prior — Free Agent (Dec 2007) [DL]
• Chad Reineke — Trade (Aug 2008)
  • Randy Wolf
• Luis Rodriguez — Waivers (Oct 2007)
• Tim Stauffer — 1st Round (2003) [DL]
• Will Venable — 7th Round (2005)
• Chris Young — Trade (Jan 2006) [DL]
  • Adam Eaton
    • Andy Ashby (RS)
      • Bruce Hurst (JMK)
      • Greg Harris (JMK)
  • Akinori Otsuka
  • Billy Killian

Minor Leagues

• Chip Ambres — Free Agent (Nov 2007)
• Josh Banks — Waivers (Apr 2008)
• Bobby Basham — Trade (Mar 2006)
  • Dave Ross
    • J.J. Furmaniak
• Adam Bass — Free Agent (Nov 2007)
• Anthony Bass — 5th Round (2008)
• Justin Baum — 7th Round (2007)
• Kyle Blanks — 42nd Round (2004)
• Matt Bush — 1st Round (2004)
• Mitch Canham — 1st Round (2007)
• Luke Carlin — Free Agent (Apr 2003)
• Cesar Carrillo — 1st Round (2005)
• Sawyer Carroll — 3rd Round (2008)
• Yefri Carvajal — Free Agent (2005)
• Brad Chalk — 2nd Round (2007)
• Drew Cumberland — 1st Round (2007)
• James Darnell — 2nd Round (2008)
• Jaff Decker — 1st Round (2008)
• Javis Diaz — Free Agent (2003)
• Allan Dykstra — 1st Round (2008)
• Logan Forsythe — 1st Round (2008)
• Ernesto Frieri — Free Agent (2003)
• Steve Garrison — Trade (Jul 2007)
  • Scott Linebrink
• Justin Germano — Waivers (Mar 2006)
• Enrique Gonzalez — Waivers (Feb 2008)
• Jeremy Hefner — 5th Round (2007)
• Sean Henn — Waivers (May 2008)
• Justin Huber — Trade (Mar 2008)
• John Hudgins — Trade (May 2006)
  • Freddy Guzman
• Chad Huffman — 2nd Round (2006)
• Cedric Hunter — 3rd Round (2006)
• Will Inman — Trade (Jul 2007)
  • Scott Linebrink
• Kellen Kulbacki — 1st Round (2007)
• Mat Latos — 11th Round (2006)
• Cory Luebke — 1st Round (2007)
• Paul McAnulty — 12th Round (2002)
• Marshall McDougall — Free Agent (Nov 2007)
• Mike Megrew — Free Agent (Jan 2008)
• Colt Morton — 3rd Round (2003)
• Brian Myrow — Free Agent (Nov 2006)
• Emmanuel Quiles — 6th Round (2007)
• Cesar Ramos — 1st Round (2005)
• Nick Schmidt — 1st Round (2007)
• Vince Sinisi — Trade (May 2006)
  • Freddy Guzman
• Eric Sogard — 2nd Round (2007)
• Craig Stansberry — Waivers (Dec 2006)
• Will Startup — Trade (Jul 2007)
  • Royce Ring
    • Ben Johnson
      • Carlos Hernandez
    • Jon Adkins
• Matt Teague — 8th Round (2007)
• Blake Tekotte — 3rd Round (2008)
• Joe Thatcher — Trade (Jul 2007)
  • Scott Linebrink
• Geoff Vandel — 34th Round (2005)
• Mauro Zarate — Waivers (Oct 2007)
• Lance Zawadzki — 4th Round (2007)