Arctic species are likely to experience rapid shifts in prey availability under climate change, which may alter their exposure to microbes and parasites. Here, we describe fecal bacterial and macroparasite communities and assess correlations with diet trophic level in Pacific walruses harvested during subsistence hunts by members of the Native Villages of Gambell and Savoonga on St. Lawrence Island, Alaska. Fecal bacterial communities were dominated by relatively few taxa, mostly belonging to phyla Fusobacteriota and Firmicutes. Members of parasite-associated phyla Nematoda, Acanthocephala and Platyhelminthes were prevalent in our study population. We hypothesized that high versus low prey trophic level (e.g. fish versus bivalves) would result in different bacterial and macroparasite communities. We found that bacterial community structure correlated to diet, with nine microbial clades enriched in walruses consuming higher trophic level prey. While no parasite compositional differences were found at the phylum level, the cestode genus Diphyllobothrium was more prevalent and abundant in walruses consuming higher trophic level prey, likely because fish are the intermediate hosts for this genus. This study suggests that diet is important for structuring both parasite and microbial communities of this culturally and ecologically important species, with potential implications for population health under climate change.