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Understanding amphibian habitat associations allows us to assess the impacts of environmental change on amphibian populations. We studied the habitat associations of five anurans in the Chihuahuan Desert of southern New Mexico, USA. We used amphibian call surveys at 36 ephemeral water bodies and recorded an index of abundance for each species. We used GIS to identify vegetation communities (e.g., creosote bush, grassland, mesquite) within a buffer zone around each water site. We used ordinal logistic regression, Akaike’s information criterion (AIC(c)), and canonical correspondence analysis to elucidate relationships between an index of anuran abundance and habitat variables. Creosote bush, mesquite, and grasses dominate the landscape in our study region. We detected Anaxyrus debilis (Green Toad) and Spec multiplicata (New Mexico Spadefoot Toad) most frequently (>70% of water bodies observed). Anaxyrus cognatus (Great Plains Toad), Scaphiopus couchii (Couch’s Spadefoot Toad), and Spec bombifrons (Plains Spadefoot Toad) were detected at about half of water bodies studied. Anaxyrus cognatus, Spec bombifrons, and Sp. multiplicata tended to co-occur at breeding sites. Anaxyrus cognatus and Sp. bombifrons were more common in mesquite habitat. Succulent desert scrub, though not common, seemed to affect Sc. couchii positively and A. debilis negatively. Spec multiplicata was more generalistic and did not show strong habitat associations. We did not find evidence that shrub encroachment has had negative impacts on the amphibian community in our study system and may even have had positive effects on anurans, especially A. cognatus and Sp. bombifrons.