During his final college season, he hit .404 with 17 home runs and 70 RBIs in only 171 at-bats,[1] while pitching 23.1 innings with a 2.70 ERA, striking out 25 and walking 6.

In the 2004 MLB draft, he was selected in the eighth round (225th overall) by the Tampa Bay Devil Rays, receiving a $275,000 signing bonus.

Hughes made his professional debut in 2005 with Short-Season A Hudson Valley, where in 58 games, he hit .279 with 8 HR and 30 RBI.

Hughes began 2007 with High-A Vero Beach, where he hit .329 with 12 HR and 57 RBI in 94 games before earning a promotion to Double-A Montgomery on August 1.

After 2008, he played in the offseason in the Arizona Fall League with Peoria, where in 27 games, he hit .394 with 5 HR, 27 RBI and 12 doubles.

Hughes began 2009 with Montgomery, where he was a Southern League All-Star, joining fellow Biscuits Jeremy Hellickson, Desmond Jennings and Eddie Morlan.

[3] On August 8, 2009, the Baltimore Orioles traded catcher Gregg Zaun to the Rays for cash or a player to be named later.

[6] Hughes was invited to spring training with the Orioles in 2010, where in 15 games, he hit .316 with 3 HR and 6 RBI before being cut on March 26.