Pyrosequencing platforms have been widely used in 16S rRNA deep sequencing of organisms sampled from environmental surveys. Despite the massive number of reads generated by these platforms, the reads only cover short regions of the gene, and the use of these short reads has recently been called into question for phylogeny-based and diversity analyses. We explore the limits of the use of short reads by quantifying the loss of information, and its effect on phylogeny. Using available nearly-full-length reads from published clone libraries and databases, and simulated short reads created from these reads, we show that for selected regions of the gene, short reads contain a surprisingly high amount of biological information, making them suitable to resolve an approximate phylogeny. In particular, we find that the V6 region is significantly poorer than the V1–V3 region in its representation of phylogenetic relationships. We conclude that the use of short reads, combined with a careful choice of the gene region used, and a thorough alignment procedure, can yield phylogenetic information comparable with that obtained from nearly-full-length 16S rRNA reads.