16S rRNA gene profiling has recently been boosted by the development of pyrosequencing methods. A common analysis is to group pyrosequences into Operational Taxonomic Units (OTUs), such that reads in an OTU are likely sampled from the same species. However, species diversity estimated from error-prone 16S rRNA pyrosequences may be inflated because the reads sampled from the same 16S rRNA gene may appear different, and current OTU inference approaches typically involve time-consuming pairwise/multiple distance calculation and clustering. I propose a novel approach AbundantOTU based on a Consensus Alignment (CA) algorithm, which infers consensus sequences, each representing an OTU, taking advantage of the sequence redundancy for abundant species. Pyrosequencing reads can then be recruited to the consensus sequences to give quantitative information for the corresponding species. As tested on 16S rRNA pyrosequence datasets from mock communities with known species, AbundantOTU rapidly reported identified sequences of the source 16S rRNAs and the abundances of the corresponding species. AbundantOTU was also applied to 16S rRNA pyrosequence datasets derived from real microbial communities and the results are in general agreement with previous studies.