Gwynn, the brother of Hall of Fame outfielder Tony Gwynn, has been the Padres' director of player personnel since December 2009.
Gwynn is in his 14th season with the Padres, and also his 27th year overall in professional baseball.
Madison has been the director of scouting since December 2009, as well, returning to the organization for his third stint with the team.
Madison and Gwynn were initially scouts with the Padres, before Madison left to become an area scout with the Pirates prior to returning to San Diego in 2005 to be the assistant to the director of scouting. Madison later spent two seasons with the Cardinals as assistant scouting director.
Last week, the team extended the contracts of assistant general managers/vice presidents Fred Uhlman Jr., and Jason McLeod. Also, the Padres promoted A.J. Hinch to assistant general manager/vice president.
Hinch had just completed his first season as director of professional scouting.
Madison and McLeod have presided over the last two First-Year Player Drafts.