Prosopis glandulosa (mesquite) is effectively nodulated by both fast-growing (FG) and slow-growing (SG) rhizobia. The distribution of indigenous, free-living, FG and SG rhizobia, and their morphological and symbiotic characteristics associated with the rooting systems of mesquite were investigated. The three warm desert ecosystems studied were an arroyo, a sand dune, and a playa in the Chihuahuan Desert of New Mexico, and a sand dune and playa in the Sonoran Desert of southern California. The FG rhizobia dominated free-living rhizobial population from 0- to 8-m depth, at the New Mexico playa. In contrast to the New Mexico playa, the surface 1 m soil under mesquite at the California playa was dominated by SG rhizobia, otherwise FG rhizobia dominated to 9-m depth. Slow-growing rhizobia dominated the lowest depths of the mesquite rooting system in both playas. Slow-growing rhizobia dominated the entire rooting zone of both sand dune ecosystems. Fast-growing rhizobia dominated the upper 2 m and SG rhizobia dominated below 2 m in the mesquite rooting zone at the New Mexico arroyo. Regression analysis indicated that the distribution of FG and SG rhizobia was related to the concentration of total soil salts (electrical conductivity) (r² = 0.20). Chi-square analysis of the distribution of colony morphologies indicated distinct rhizobial populations in each ecosystem. The FG rhizobial population at the New Mexico playa was highly effective and had a high frequency of Hup+ phenotypes. The FG rhizobia isolated from the arroyo were, in contrast, less effective and had a low frequency of Hup+ phenotypes. The SG rhizobial population at the New Mexico dune system was, in contrast, mainly ineffective and had a low frequency of Hup+ phenotypes. The relationship between the variable distribution of FG and SG rhizobia and environmental factors associated with the ecosystems is discussed.