Evaluating the biodiversity of microbial communities remains an elusive task because of taxonomic and methodological difficulties. An alternative approach is to examine components of biodiversity for which there exists a reasonable chance of detecting patterns that are biologically meaningful. One such alternative is functional diversity. We propose a procedure based on the Biolog identification system to quickly, effectively, and inexpensively assess aspects of the functional diversity of microbial communities. The numbers and types of substrates utilized by bacterial communities, as well as the levels of activities on various substrates and patterns of temporal development, constitute an information-rich data set from which to assess functional diversity. Data from six plant communities (black grama grassland. Sporobolus grassland, creosotebush bajada, herbaceous bajada, mesquite-playa fringe, and playa grassland) located along an elevational and moisture gradient at the Jornada Long-Term Ecological Research site in the northern Chihuahuan Desert, are analyzed to illustrate the procedure and its relevance to biodiversity. Our analyses demonstrate that the Biolog system can detect considerable variation in the ability of microbial communities to metabolize different carbon compounds. Variation in substrate use was compartmentalized differently along the moisture gradient. Differences in functional diversity were dependent upon the class of carbon sources (guild-specific results). A multifaceted approach to biodiversity that comprises both functional and taxonomic perspectives represents fertile ground for future research endeavors.