The influence of landscape structure on distribution patterns of bats remains poorly understood for many species. Understanding the influences of island size and isolation on probabilities of species occurrence provides potential insight for conservation of bats by identifying how species may vary in persistence and immigration abilities. We investigated the influence of island area and isolation on probability of occurrence of 6 bat species on 32 islands in a desert island archipelago in Baja California, Mexico. We compared 5 a priori models to explain patterns of island occupancy, including random patterns, minimum area effects, maximum isolation effects, additive area and isolation effects, and compensatory area and isolation effects. Five insectivorous species displayed minimum area thresholds on incidence, suggesting island occupancy by these species is limited by resource requirements. Islands smaller than 100 ha typically did not support occupancy or use by insectivorous bats, except at minimal isolation distances. Minimum area thresholds on bat incidence mirror those found for birds in the same archipelago and are likely linked to changes in habitat structure on islands too small (ca. < 200 ha) to support formation of complex geomorphological structures, such as arroyos. Probability of occurrence of insectivorous bats tended to decrease at moderate distances, suggesting greater sensitivity to isolation than previously expected for bats. Distributions of two non-insectivorous species (Leptonycteris curasoae and Myotis vivesi) were not influenced by island size and isolation, suggesting differences in foraging habits may have important implications for understanding distribution patterns of bats.