Vertical profiles of polychlorinated dioxins and microbial biomass including "Dehalococcoides" populations in cores of sediment of Lake Suwa, Japan, were investigated. The core samples were analyzed in 3-cm intervals at 0-15 cm and 50 cm, where a sharp gradient of Eh from 5 to −110 mV with depth occurred. The concentration of polychlorinated dioxins was relatively constant at 0-15 cm, ranging from 7.6 to 8.3 ng (7.0-9.2 pg-TEQ [toxic equivalent]) g −1 dry wt, but decreased sharply at 50 cm. The total bacterial count was in the order of 10 8 to 10 9 g −1 dry wt, being highest at 3-6 cm and decreasing in the deeper sediment. A similar vertical profile was found for respiratory quinones with larger amounts of ubiquinones than menaquinones at 0-15 cm. Quantitative real-time PCR with a specific primer set showed that "Dehalococcoides" and its phylogenetic relatives occurred in the order of 10 4 g −1 (dry wt) at 0-12 cm but were absent at 50 cm. The amplified clones showed 91-100% similarity (mostly <94%) in sequence to a well-known dioxin-dechlorinating organism, "Dehalococcoides" sp. strain CBDB1. These results suggested that the surface sediment up to a depth of 12 cm provided favorable conditions for the growth and activity of both aerobic and anaerobic microorganisms including "Dehalococcoides". It is likely that a wide variety of "Dehalococcoides" and phylogenetic relatives thereof are omnipresent even in sediment with low levels of dioxins and play the primary role in dechlorinating organohalorides over a relatively wide range of Eh.