The vertical distribution of phototrophic and non-phototrophic microorganisms was examined in 2 saltern evaporation ponds with salinities of 156 and 206 g l -1. The biogeochemistry of these 2 ponds was examined using microsensors for oxygen, pH and sulfide. These measurements showed that net rates of oxygen production/consumption were significantly higher at a salinity of 156 than at 206 g l -1. The distribution of phototrophic microorganisms was studied by microscopy, which revealed several differences between the 2 crusts. The relative amounts of Bacteria, Archaea, sulfate reducers and methanogens were studied by real-time quantitative PCR amplification of genes for 16S rRNA, dissimilatory sulfite reductase (DSR), and methyl coenzyme M reductase (MCR). Sulfate reducers and methanogens were detected only in the deepest part of the phototrophic zone and below. Sulfate reducers were most abundant in the zone just below the phototrophic layer, where the DSR gene copy number was ~1.5% that of the 16S rRNA gene copy number. Methanogens were much less abundant than sulfate reducers, and the number of MCR gene copies never exceeded 0.1% of the number of 16S rRNA gene copies. Methanogens were less abundant at a salinity of 206 than at 156 g l -1. Inter-pond and vertical variations in the composition of methanogenic and sulfate reducing communities were further characterized by DGGE analysis. The detected sulfate reducers were affiliated with 4 different phylogenetic groups that included members of the Desulfovibrionales, relatives of Desulfotomaculum, and 2 deeply branching groups with no close cultured relatives. The detected phylotypes were distributed in a distinct pattern in the crust according to both biogeochemical regimes and salinity. Methanogens were all affiliated with the known halophilic genera Methanohalophilus and Methanohalobium.