Organic material is degraded anaerobically by a complex community of microbes making up the anaerobic food chain. This community was examined in methane‐rich sediments of the Beaufort Sea, Alaska, using metagenomic sequencing, along with tag pyrosequencing and quantitative polymerase chain reaction analyses of 16S ribosomal ribonucleic acid genes. The goal of the study was to examine the relative abundance and taxonomic composition of organisms making up different parts of the anaerobic food chain. The metagenomic data suggested that genes for producing acetate via fermentation (“acetate fermentation”) were more common than genes producing other fermentation by‐products, but acetate fermentation genes made up only 32% of all genes for fermentation pathways while genes for fermentation to ethanol accounted for 27%. The genes for the production of other compounds, including propionate (15%), butyrate (11%), lactate (4%), and hydrogen gas (11%), were also often abundant. Similar results were observed when the same approach was used to analyze metagenomic data previously collected from two low‐latitude systems with methane‐rich sediments. In all of these sediments, genes for pathways producing organic acids, ethanol, and hydrogen gas were about 30‐fold more abundant than the genes for sulfate reduction and methanogenesis, processes which consume those compounds. Our results suggest that the type and abundance of fermentative microbes potentially affect the taxonomic composition of sulfate‐reducing bacteria and methanogenic archaea and rates of organic carbon mineralization by the anaerobic food chain.