Mission San Juan Bautista may refer to any of the following missions, all of which are named for John the Baptist:
- Mission San Juan Bautista, in San Juan Bautista, California, United States
- Misión San Juan Bautista Malibat, near Loreto, Baja California Sur, Mexico
- Mission San Juan Bautista (Mexico), in Guerrero, Coahuila, Mexico
This disambiguation page lists articles associated with the title Mission San Juan Bautista.
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