San Jacinto authorities started investigating the crime in July 2011. They said Alejandro Rios, 51, fled the area after the assaults were reported to police.
Detectives said Rios lived with the two young girls and the alleged sexual assault happened over the span of several months.
Police arrested Rios Wednesday after finding out that he worked at an automotive repair shop in Banning. He was booked for several sexually-related crimes involving minors.