Microbial communities from five wells in a Canadian oil field were characterized by sequencing 16S rRNA and cpn60 gene amplicons. Analysis of 16S rRNA amplicon sequences using the RDPipeline and the Phoenix 2 pipeline showed that amplicons representing Ralstonia, Arcobacter, Sulfurospirillum, Methanohalophilus, Methanocalculus and Methanolobus spp. were abundant in most samples. Amplicons derived from Bacillus and some other genera were detected in samples as well. Analysis of cpn60 sequences confirmed that amplicons derived from Sulfurospirillum, Methanolobus and Bacillus spp. were well represented, and showed that a bacterium highly similar to biosurfactant producing Bacillus mojavensis represented the genus Bacillus. In addition, analysis of cpn60 sequences showed that amplicons derived from the Deltaproteobacteria, particularly Pelobacter carbinolicus, were abundant. However, analysis of cpn60 sequences failed to detect amplicons representing Ralstonia spp. or other representatives of the Betaproteobacteria, indicating possible PCR bias. Our findings suggest that gaps resulting from shortcomings of 16S rRNA and cpn60 gene amplification and analytical systems can be overcome through simultaneous targeting of these conserved genes.