The microbially mediated anaerobic oxidation of methane (AOM) is critical for regulating the flux of methane from the ocean. AOM is coupled to sulfate reduction (SR) in many anoxic marine environments, which has been extensively studied at cold seeps, hydrothermal vents, and the sulfate-methane transition zone at the seafloor. Sulfate-dependent AOM is performed by specialized groups of anaerobic methane-oxidizing (ANME) archaea, which are thought to form consortial relationships with sulfate-reducing bacteria (SRB). Certain ANME and SRB groups have been shown to occupy different ecological niches in both hydrocarbon seep and hydrothermal vent sediments. However, the environmental parameters that select for certain phylogenetic variants across these hydrocarbon-rich marine ecosystems are still unknown. In this study, we generated the largest dataset to date of 16S rRNA gene sequences for these uncultivable deep sea microorganisms using Illumina sequencing. Sediment strata were collected from the cold seeps of Hydrate Ridge, metalliferous sediments of Juan de Fuca Ridge, and organic-rich hydrothermal sediments of Guaymas Basin. We then used the Illumina MiSeq platform to assess archaeal and bacterial richness, diversity, and taxonomic composition followed by phylogenetic analyses of ANME and SRB phylotypes across environmental gradients and geographic ranges. Environmental metadata were used to establish the relationships between ANME and SRB phylotype distribution and environmental gradients as well as the extent of these functional groups in different hydrocarbon-rich ecosystems. Our results indicate that physicochemical constraints, particularly temperature and substrate availability, drive the distribution of different ANME and SRB ecotypes and the associated communities in spatially separated sites.