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Amphibians are often thought to have a metapopulation structure, which may render them vulnerable to habitat fragmentation. The red-spotted toad (Bufo punctatus) in the southwestern United States and Mexico commonly inhabits wetlands that have become much smaller and fewer since the late Pleistocene. This study tests two predictions based on metapopulation theory, that the incidence of habitat patch occupancy is directly related to patch size and that it is inversely related to patch isolation, and a third, potentially competing hypothesis, that patch occupancy is influenced by local environmental conditions. In a 20 000 km(2) area of the eastern Mojave Desert, 128 potential habitat patches (primarily springs) were identified and surveyed for local environmental characteristics and presence/ absence of B. punctatus. Patch size metrics reflected extent of water and riparian vegetation of several types. Patch isolation metrics were based on nearest-neighbor distances, calculated both as Euclidian distance and distance via connecting drainage channels. B. punctatus was found at 73% of the sites, including all of the 16 historic (pre-1970) sites. Patches were generally quite small, with water extending a median distance of only 200 m and median area of 72 m. Median nearest-neighbor distances among patches were 1.8 km Euclidian distance (range: 0.4-22.0 km) and 6.8 km via drainage channels (range: 0.5-64.9 km). Based on stepwise multiple logistic regression, the incidence of patch occupancy increased significantly with patch size and was also significantly related to elevation, latitude, and four metrics that were associated with rocky terrain, periodic scouring water flows, and ephemeral water. In contrast, incidence of patch occupancy was not significantly related to patch isolation. These findings are consistent with a "patchy population" model, rather than the classical equilibrium metapopulation model, implying frequent dispersal among patches and virtually no local extinctions. We speculate that B. punctatus in the Mojave Desert today occurs primarily in a patchy population or populations within mountain ranges that are isolated from patchy populations in other ranges. The influence of local environmental characteristics on patch occupancy demonstrates the importance of including patch quality metrics in tests of predictions for patch occupancy based on metapopulation theory.