Police says Flores was an acquaintance of the victims, 25-year old Kristen Evans Kennedy, of Chicago, and 28-year-old Jennifer Evans.
Firefighters responding to a fire Friday evening found the women dead in the bathroom of Evans' home. Police believe the fire was set to cover up the killings.
Flores is facing murder, rape and arson charges. He is being held without bond.
The funerals for the two victims were held Wednesday.