The vandalism is being treated as a hate crime, San Jose police Officer Jermaine Thomas said.
Staff at Trinity Presbyterian Church and Indonesian Christian Church, both located at 3151 Union Ave., reported the vandalism early Monday morning.
Thomas said the markings were found on the signs for both of the churches.
The vandalism was committed late Sunday or early Monday and investigators are still working to identify a suspect.
Anyone with information on the case is asked to call the Police Department's assault unit at (408) 277-4161.