A commonly observed preferential association was quantified between mature native mesquite (Prosopis articulata) trees and the seedlings of six cactus species (Pachycereus pringlei, Opuntia cholla, Lophocereus schottii, Machaerocereus gummosus, Lemaireocereus thurberi, Mammilaria sp.) in a previously-disturbed area of the Sonoran Desert of Baja California, Mexico. We hypothesized that, in addition to more favorable edaphic factors, the inoculum potential of beneficial vesicular-arbuscular mycorrhizal (VAM) fungi was higher, and therefore, more favorable for cactus seedling establishment under the mesquite tree canopy (UC) compared to adjacent barren areas (BAs) away from the trees. In the greenhouse inoculum potential assays, VAM fungi were detected in onion (Allium cepa) trap plants from all soil samples regardless of collection site, but cardon cactus (P. pringlei) trap seedlings formed no VAM even after 6.5 months. Test soils were further used to preinoculate new onion seedlings transplanted into pots, to serve as nurse plants to inoculate adjacent cardon seedlings by vegetative transfer. After 15 months, cardon seedlings did develop slight VAM colonization, confined exclusively to the outermost cortical layers. Examination of test soils for spores or root fragments revealed very few to none, and spore production on onion trap plant roots was also sparse even though colonization was high. Analysis of UC and BA soils revealed that the water holding capacity, nutrient content, cation exchange capacity, total carbon, and total nitrogen contents of the UC soils were all higher than those of the BA soils. Since the VAM inoculum density in this study was not different between sites under and away from the mesquite tree canopy, we concluded that VAM inoculum density is not the primary factor for the establishment of cactus seedlings and that edaphic factors probably play a more important role. Our results suggest, however, that VAM inoculum potential in these hot desert soils, although relatively low, is probably maintained in the upper layers by means of hyphal fragments rather than spores.