Evolution acts to shape genetic variation within populations. However, in microbial communities, it is often surprisingly difficult to characterize what the “population” actually represents. This makes it hard to interpret the diversity often observed in microbial communities. To what extent is diversity within a microbial species (or operational taxonomic unit, typically defined to span ~3% 16S rRNA sequence divergence) representative of one population occupying a single ecological niche? Do multiple sequence clusters in a given population represent distinct functionally diverse strains? And by how much does genetic exchange blur the boundaries of strains and species? On page 1019 of this issue, Rosen et al. (1) show that rapid genetic exchange maintains extensive diversity of mosaic genomes in a cyanobacterial biofilm community, despite the action of selection on many individual loci.