The digestive tracts of fishes contain a diverse set of gut associated microbiota known to contribute to many functions of the fishes' biology. Furthermore, it has been suggested that divergence in diets between two species is also associated with shifts in gut associated microbiota. Herein, we describe and compare the diet and gastrointestinal microbiota of two closely related combtooth blennies, Scartella cristata and Chasmodes saburrae (family Blenniidae) from Florida, USA. The diets of the two species were significantly different; C. saburrae consumed benthic or epiphytic crustaceans, while S. cristata consumed plants and detritus. Similarly, the gastrointestinal microbiota were significantly different between the two species. Gammaproteobacteria were the most abundant class identified in all samples, regardless of species, but S. cristata had higher relative abundances of Vibrionaceae, Methylococcaceae, and Fusobacteriaceae than did C. saburrae. These findings suggest that closely related species with vastly different diets results in distinct gastrointestinal bacterial communities. Lastly, digestive tract length and diet of these blennies were correlated with specific gastrointestinal microbiota, providing further evidence that these two factors may play a critical role in shaping gut microbial communities. Further research is necessary to tease apart the gut associated microbiota and transient microbiota and determine the role they play in digestion and trophic status of these fishes.