Steven Michael Garcia is being held on charges of forced entry and commercial burglary at Hordin's Income Tax Service and Harold's Jewelry at 164 Main St.
Harold's Jewelry had about $500,000 in loss of jewelry, police said.
Investigators say the crime scene revealed several items that contained trace DNA, and those items were submitted to a Department of Justice crime lab that led to the identification of Garcia.
Los Altos police, along with members of the Santa Clara and San Jose police departments, executed a search warrant Monday on Garcia's San Jose home, and seized several jewelry items, as well as electronic devices and construction tools.
Harold Yan, the owner of Harold's Jewelry, positively identified several items of jewelry that were seized from the home, according to police.
An arrest warrant was also obtained for Garcia, who was already in custody in Milpitas for unrelated criminal matters.
He is currently being held on two charges of commercial burglary and one count of grand theft, with a total bail amount of $50,000, police said.