The possibility of quantifying in situ levels of transcripts for dissimilatory (bi)sulfite reductase (dsr) genes to track the activity of sulfate-reducing microorganisms in petroleum-contaminated marine harbor sediments was evaluated. Phylogenetic analysis of the cDNA generated from mRNA for a ca. 1.4 kbp portion of the contiguous dsrA and dsrB genes suggested that Desulfosarcina species, closely related to cultures known to anaerobically oxidize aromatic hydrocarbons, were active sulfate reducers in the sediments. The levels of dsrA transcripts (per mug total mRNA) were quantified in sediments incubated anaerobically at the in situ temperature as well as in sediments incubated at higher temperatures and/or with added acetate to increase the rate of sulfate reduction. Levels of dsrA transcripts were low when there was no sulfate reduction because the sediments were depleted of sulfate or if sulfate reduction was inhibited with added molybdate. There was a direct correlation between dsrA transcript levels and rates of sulfate reduction when sulfate was at ca. 10 mM in the various sediment treatments, but it was also apparent that within a given sediment, dsrA levels increased over time as long as sulfate was available, even when sulfate reduction rates did not increase. These results suggest that phylogenetic analysis of dsr transcript sequences may provide insight into the active sulfate reducers in marine sediments and that quantifying levels of dsrA transcripts can indicate whether sulfate reducers are active in particular sediment. Furthermore, it may only be possible to use dsrA transcript levels to compare the relative rates of sulfate reduction in sediments when sulfate concentrations, and possibly other environmental conditions, are comparable.