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Understanding the biodiversity of functionally important communities in Earth’s ecosystems is vital in the apportionment of limited ecosystem management funds and efforts. In southern California shrublands, which lie in a global biodiversity hotspot, biological soil crusts (BSCs) confer critical ecosystem services; however, their biodiversity remains unknown. In this study, six sites (n = 4 each, 25 m(2)) were established along a mediterranean shrubland environmental gradient in southern California. Here, the biodiversity of all BSC-forming lichens and bryophytes was evaluated, related to environmental traits along the gradient, and compared to species richness among North American ecosystems supporting BSCs (data from previous studies). In total, 59 BSC-forming lichens and bryophytes were observed, including the very rare Sarcogyne crustacea, a rare moss, and five endemic lichen species. Over half (61%) of the species observed were found at a single site. Along the gradient, species evenness of late-successional BSC was related to dew point and elevation, and both evenness and richness were related to distance to coast. Using an ordination analysis, five distinct late-successional BSC communities were identified: Riversidian, Spike moss, Casperian, Alisian, and Lagunian. Twenty-five lichens and 19 bryophytes are newly reported for North American BSC-forming organisms, now comprising similar to 1/2 of the North American total. BSCs in North American hot and cold deserts were approximately 4.0 and 2.4 times less species rich than BSCs found in southern California shrublands, respectively. Given the anthropogenic impacts on quality and distribution of California mediterranean shrublands, our results show that these sites represent important refugia of BSC species in this globally important region.