Direct molecular analysis of the composition and structure of geothermal cyanobacterial mat communities has revealed diversity patterns suggesting that adaptive radiation and geographic isolation are the important drivers of cyanobacterial diversification. It is clear that 16S rRNA sequence variation cannot detect all ecological or geographic populations (ecotypes and geotypes, respectively), but it remains unclear what level of molecular resolution is required to do so. These empirical patterns are consistent with periodic selection theory for the evolution of prokaryotic populations, which predicts that adaptation and/ or geographic isolation lead to terminal evolutionary clades with discrete ecological or geographic character. These clades, if long standing and not subject to geographic effects, may be detected as molecular sequence clusters to identify putative ecotypes within a community. An evolutionary simulation, called Star, is used to predict from the features of sequence data how to demarcate such sequence clusters. We are developing methods to determine whether the ecological diversity in mat communities is best predicted by periodic selection theory or by alternative theories based on rapid evolution of ephemeral ecotypes and/or the effects of geographic isolation.