Wild bees provide the essential ecosystem service of pollination, which may be particularly important in island systems that host rare and endangered plants. Identifying and protecting nesting habitat of wild bees is critical for successfully conserving these pollinators and their pollination services, but characterization and delimitation of nesting habitat receives relatively little attention in the literature compared to description of floral interactions. Such data on wild bee nesting is necessary for creating effective conservation strategies that benefit the stability of ecosystem services, as well as promote the populations of both pollinators and plants. On San Clemente Island, we identified the locations of 50 bee nest sites. Bees from 12 sites were collected and identified as Diadasia bituberculata (n = 9), D. opuntiae (n = 2), and Anthidium collectum (n = 1). We characterized sites by vegetation cover and soil type: half (54%) of the sites were found in maritime desert scrub–prickly pear phase vegetation, and most (82%) were associated with loam-type soil. Here we provide the first descriptions of ground-nesting bee habitats on San Clemente Island and suggest that conservation of bee nesting habitat could be incorporated into existing avian and plant conservation management efforts in these shared habitats.