Magnetotactic bacteria (MTB) contain membrane-bound magnetic iron minerals and are globally abundant in the suboxic/anoxic portions of chemically stratified marine and freshwater environments. However, their population dynamics and potential quantitative contribution to the biogeochemical cycles that they influence (iron, sulfur, carbon) have not been previously considered. Here we report the first quantitative description of the distribution of individual species of magnetite- and greigite-producing MTB in a natural system. We developed a quantitative polymerase chain reaction assay targeting 16s rRNA genes to enumerate four major groups of marine MTB, and applied the assay to samples collected with respect to geochemical parameters during summer 2003 in seasonally stratified Salt Pond, MA. Using catalysed reporter deposition-fluorescent in situ hybridization, we also show that a large greigite-producing bacterium is distantly related to Thiomicrospira pelophila in the Gammaproteobacteria. Ribosomal RNA copy numbers obtained with quantitative polymerase chain reaction indicate that MTB comprise up to 10% of total Bacteria and that each organism has a characteristic distributional profile with respect to the chemocline.