Jed Hoyer is heading west. After seven years in the Boston Red Sox front office, including a brief stint as co-general manager with Ben Cherington during Theo Epstein’s leave in 2005, Hoyer finally has earned a GM position of his own with the San Diego Padres.

According to SI.com’s Melissa Segura, a front office source indicated that the Padres will name the 35-year-old Hoyer their head of baseball operations, supplanting longtime general manager Kevin Towers, who was fired on Oct. 3 after 14 seasons with the team.

The hiring of Hoyer adds an ironic twist to a developing saga between the Red Sox and Padres front offices. Epstein was a disciple of Towers’ in San Diego before becoming Boston’s general manager, and now Epstein’s own protégé is taking over for the man who helped bring him into the league. 

Hoyer was known as one of the more talented front office assistants in the majors while with the Red Sox and quickly became one of the leading candidates for in San Diego after Towers was dismissed. Padres owner Jeff Moorad’s decision reportedly came down to Hoyer and Dodgers assistant general manager Kim Ng, and the team went with Epstein’s right-hand man in the end.

The Padres finished fourth in the NL West this past season with a record of 75-87, so Hoyer will have his work cut out for him as he tries to bring postseason baseball back to San Diego for the first time since 2006. 

But Hoyer also inherits a tidy financial situation from Towers, with a cheap superstar to build around in first baseman Adrian Gonzalez, an excellent trade chip in closer Heath Bell and only one bad contract (that of pitcher Chris Young, who is scheduled to make $6.25 million in 2010) remaining on the payroll. If Hoyer uses the Friars’ remaining budget wisely, the Padres could climb back into contention for the division crown within a couple of years.

Hoyer’s days in Boston should have taught him well. Now we’ll find out if Epstein passed on his knowledge as well as Hoyer’s predecessor in San Diego did.