Recent reports of pollinator declines have revealed a need to better document how anthropogenic disturbances and biogeography jointly influence wild pollinator communities. Here, we examine the effects of urbanization-induced habitat fragmentation on the native bee fauna inhabiting coastal sage scrub habitats of San Diego County, California, USA, a hotspot of bee biodiversity. Pitfall trapping in natural reserves and scrub habitat fragments yielded 70 native bee species or morphospecies, and revealed that bee species richness was lower in fragments than in reserves. However, fragments and reserves harbored bee assemblages similar in relative abundance, evenness, and community composition. Our samples yielded multiple species that are poorly represented in four of the leading institutions with collections of native bees from the southwestern United States, as well as 16 species represented only by specimen records from outside of San Diego County. Our results highlight the importance of continued efforts to document bee assemblages in under-studied regions with respect to their faunal distribution and basic taxonomy, as well as how they are impacted by anthropogenic disturbances such as habitat fragmentation. We also discuss the value of analyzing vouchered pitfall samples for non-target taxa captured incidentally.