The processes underlying the phylogenetic structure of the biotic communities are typically scale-dependent and thus often poorly resolved. Illustrated by the study of macroorganisms, it is suggested that the relative influence of ecological processes on the phylogenetic structure of the communities can be inferred by the geographical definition of the species pools. However, given the high dispersal ability of microbes, the spatial delineation of the species pool may not be that practical for microbial taxa. This idea is supported by the observational data on bacteria along an elevational gradient. Significant negative values of standardized effect size of the mean nearest taxon distance were consistently observed for different sized species pools considered. Reviewing the reports on microbial phylogenetic structure so far, we suggested that the ‘habitat species pools’ are perhaps more important for microbes than spatial delineated ‘regional species pools’.