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The southwestern myotis is found from the southern two-thirds of Arizona and New Mexico south into central Mexico. This bat often lives in ponderosa pine forests, oak woodlands, mesquite, chaparral, and pinon-juniper scrub. It is especially abundant where these habitats occur near rocky cliffs and water. Radio-tracking studies in the Chiricahua Mountains of southeastern Arizona revealed maternity roosts of up to 30 individuals living in small tree hollows, predominantly in sycamore.
Other roosting cavities were in Arizona white oak and ponderosa pine. Most roosts were in riparian habitat adjacent to water. In northern Arizona, maternity roosts were also in cavities of both living and dead Gambel oak, and under the bark of ponderosa pine snags. Winter range and feeding behavior are largely unknown. However, its apparent preference for habitat adjacent to cliffs suggests possible reliance on cliff-face crevices for hibernation.