A growing body of evidence suggests analysis of 16S rRNA gene sequences provides only a conservative estimate of the actual genetic diversity existing within microbial communities. We examined the less conserved internal transcribed spacer (ITS) region of the ribosomal operon to determine the impact microdiversity may have on our view of marine microbial consortia. Analysis of over 500 ITS sequences and 250 associated 16S rRNA gene sequences from an oceanic time series station in the San Pedro Channel, California, USA, revealed that the community in this region is com- posed of large numbers of distinct lineages, with more than 1000 lineages estimated from 3 clusters alone (the SAR11 clade, the Prochlorococcus low-B/A clade 1, and the Roseobacter NAC11-7 clade). Although we found no instances where divergent ITS sequences were associated with identical 16S rRNA gene sequences, the ITS region showed much greater pairwise divergence between clones. By comparison to our 16S rRNA gene-ITS region linked database, we were able to place all ITS sequences into a phylogenetic framework, allowing them to act as an alternative molecular marker with enhanced resolution. Comparison of SAR11 clade ITS sequences with those available in GenBank indicated phylogenetic groupings based not only on depth but also on geography, potentially indicating localized differentiation or adaptation.