Alston was terminated shortly after returning to work following two years of active military duty, part of which he spent in Iraq.
According to the complaint, the company fired Alston after accusing him of stealing paint, a charge he denies.
The Justice Department said the firing violates the Uniformed Services Employment and Reemployment Rights Act of 1994, a law that prohibits discrimination against employees because of their military obligations.
A message left at the Hawthorne Paint Co. after business hours Monday was not immediately returned.
The federal lawsuit says Alston returned to work at Hawthorne Paint in January 2007 after being on active duty from June 2004 to June 2006. Before returning to work, Alston spent several months attending medical appointments related to injuries he suffered in Iraq.
The Justice Department's Civil Rights Division said it filed 12 USERRA suits last year, the largest number since receiving enforcement authority in 20004.