Ruben Ceballos Cobarruvias, 47, was arrested at about 10:45 a.m. Tuesday after an investigation determined that he allegedly molested two minors a decade ago at VHM Christian School, sheriff's Deputy Ryan Kennedy said.
He had worked at the school since 2001, according to the sheriff's office.
Cobarruvias may also have had contact with children at Monterey Bay Academy in Watsonville where he parked the school bus he drove for VHM Christian School students, Kennedy said.
Both schools are run by the Seventh-day Adventist Church.
Investigators believe there may be more molestation victims and are asking anyone with information on the case to call the Santa Cruz County Sheriff's Office at (831) 454-2311.
VHM Christian School Principal Judy Seagreaves said in a statement that Cobarruvias has been placed on administrative leave and that the school will cooperate with deputies in the investigation.
"We consider the children enrolled in VHM Christian School to be precious gifts entrusted to our care; protecting them from harm is among our greatest concerns. Our prayers go out to everyone involved in it," she said.