Oases on Mexico's Baja California peninsula harbor farms and gardens which largely feature crops first introduced by Jesuit missionaries (1697–1768). These spring-fed agricultural landscapes are currently managed as diverse agroecosystems with original heritage food crop species as well as newer crop and livestock introductions. These isolated landscapes are relict sanctuaries for unique desert crop varieties and farming systems that may be important for in situ conservation of agrobiodiversity and crop resources. Historical records in 1774 describe 21 original perennial crop species introductions in cultivation on the peninsula just after the Jesuit expulsion. This research expands rapid-assessment surveys conducted in nine mission oasis sites on the peninsula in 2010 through in-depth surveys of Mission era and total perennial crop species richness and relative frequency in twelve Jesuit mission oases. In all, 241 large field-gardens were surveyed with eighty-nine total perennial crop species cultivated in the mission oases. Species-area and rank-abundance relationships were calculated to determine patterns of inter and intra-oasis agrobiodiversity. A high persistence of Mission era species indicates that these oases serve as agrobiodiversity refugia, or protected source areas for heritage perennial crop species. The cultural and agricultural islands of the oases should be considered as an archipelago of interconnected sites for the long-term resilience of the region's farming and food systems.