Graduation date: 2007Island biogeography has strongly influenced the study of biodiversity because archipelagos provide natural model systems for investigating patterns of diversity and the processes that shape ecological communities. I investigated the influence of area and isolation of islands (n = 32) in the Gulf of California, Mexico on patterns of richness, nestedness, and incidence of desert bats to determine factors important in shaping community structure and patterns of occurrence of bats in a naturally insular landscape. Species richness of bats was positively influenced by island size and declined with isolation from the Baja peninsula in two distinct subarchipelagos. Southern islands, which are associated with greater density of vegetation from summer rainfall, supported more species than dry, barren islands in the northern subarchipelago, suggesting that both area and habitat characteristics contribute to species richness of bats. Community composition of bats was nested by area and isolation, such that species found on smaller and more isolated islands were subsets of communities found on large, less isolated islands that harbored higher richness. The influences of area and isolation on community nestedness suggest species differ in immigration and persistence rates on islands. Bat communities were also nested at 27 sites in coastal habitat on the Baja peninsula, indicating that nestedness may occur in contiguous habitats that lack immigration and extinction filters. Probability of species occurrence on islands was influenced by area for five species of insectivorous bat (Pipistrellus hesperus, Myotis californicus, Macrotus californicus, Antrozous pallidus, and Mormoops megalophylla), suggesting occupancy of islands by these species is limited by resource requirements. The threshold of island size for occupancy of most species was ca. 100 ha, which is similar to area thresholds of incidence for many landbirds in the same archipelago. Isolation also influenced incidence of insectivorous bat species. My research shows that area and isolation influence both community structure and occupancy of bat species in a near-shore archipelago. My results raise important questions about connectivity and persistence of populations of bats in isolated habitats, especially when patch size is small.