Raul Villalobos, 40, and Juan Valencia, 39, were found on Aug. 22 in a wooded part of a residential neighborhood, Indianapolis police said.
One of the men showed signs of having suffered head trauma prior to his death, although police could not say which one.
Officer Mike Hewitt of the Indianapolis Metropolitan Police Department said that there was nothing to indicate that the two men had been living in Indianapolis before they died.
The men were identified using dental records and through a missing person's database, Indianapolis police said.
According to San Jose police, Villalobos was reported missing on July 6 and Valencia on Aug. 24. Both men were reported missing by family members.