Mesopelagic fishes are important consumers of zooplankton and are the prey of oceanic predators. Some mesopelagic fishes (e.g., Myctophidae) undertake a diel vertical migration where they ascend to the near-surface waters during the night to feed and descend into the depths during the day to avoid predators. Other mesopelagic fishes (e.g., Sternoptyx) remain at depth throughout the day. Although fishes of different depths eat different prey items, vertical migration likely leads to overlap in species distributions and diet, potentially linking trophically transmitted surface and deep-pelagic parasite communities. The study of gut contents and parasites can yield insights into the trophic dynamics occurring within these assemblages. We examined the diet and parasite assemblages of 18 mesopelagic fish species in the Gulf of Mexico. We identified six different feeding guilds within this assemblage based on gut contents: copepods, copepods/mesozooplankton, copepods/ostracods, gelatinous zooplankton, generalist mesozooplankton, and upper-trophic level items such as fish. Although parasite abundances were generally low, mesopelagic fishes hosted a diverse assemblage of parasites, including larval and adult digeneans, larval cestodes, larval nematodes, and larval acanthocephalans. The parasite assemblages differed significantly among host feeding guilds. Large, vertically migrating fishes that predate upon fish and squid communities had a greater likelihood of having one or more parasites compared to the other fishes examined. Results from this study suggest that upper-trophic level mesopelagic fishes are more regularly involved in the life cycle of parasites in the Gulf of Mexico than zooplanktivorous fishes.