In estuarine sediments, dissimilatory sulfate reduction is regarded as the major anaerobic microbial respiration process. The communities of sulfate-reducing microbes (SRM) from two different sedimental habitats in Gamo and Idoura Lagoons were examined along with environmental factors indicating spatial or temporal characteristics. Sediment samples were obtained from 3 stations in each lagoon. Genomic DNA was extracted from the sediment. PCR amplification specific for SRM possessing dsrB gene was performed and PCR products were applied for DGGE analysis. The DGGE band patterns were used for cluster analysis, analysis of similarity and canonical correspondence analysis (CCA). There are both common bands and site specific bands. From multivariate analyses, it seemed that band patterns were divided spatially rather than temporarily. Bray-Curtis similarity was significantly different between lagoons and CCA indicated C/N ratio of sediments was the significantly effective factor. These results imply that the C/N ratio of loading organic matter might be one of the most important factors to determine the SRM community structure in lagoon sediments.