In arid ecosystems, biological soil crusts closely interact with microarthropod communities. Together, both communities play one of the most important environmental services: decomposition of organic matter. In a desert scrub in the southern Baja California Peninsula of Mexico, microarthropod communities were correlated to biological soil crusts and the way soil properties influence distribution of the microarthropods. Twenty five soil samples were taken from 3 site types: without crusts (10), with crusts (10), and eroded surfaces (5). Microarthropods were extracted; specimens were identified to family level and feeding groups were identified. Of the 4 682 microarthropods within 40 taxa, Prostigmata had the greatest richness. The lack of plant coverage at eroded sites seems to affect micro-environmental conditions, so that no microarthropods were found at these sites and biological soil crusts were simple in structure. Among desert scrub, biological soil crusts were complex in structure, and edaphic properties were more favorable for microarthropods to thrive. Specific dissimilarities in community structure of microarthropods for each microhabitat were related to feeding preferences of each taxa.