- Baha'i Faith San Marcos
- Calvary Chapel San Dieguito
- Calvary International Fllwshp
- Crosswind Community Church
- Faith Tabernacle Apostolic Inc
- First Southern Bapt Chr
- I AM Temple Of San Marcos
- Jehovah's Witnesses
- Meadowlark Community Church
- Movement
- North Coast New Thought Rlg
- Rancho Del Rey Church
- San Marcos Chr-Religious Scien
- San Marcos Lutheran Church
- St Mark's Roman Catholic Chr
- Summit Christian Church
- Templo Cristiano Alfa Y Omega