Background The coevolution between hosts and their gut microbiota arises as a promissory research program that could explain diversity patterns. The fishes of the cichlid family are an ideal model to evaluate coevolution due to their spectacular radiation. In particular, the neotropical genus Herichthys represents a great study case of study since it includes species with wide and narrow distributions, with several feeding habits as well as species that arose allopatrically and truly sympatrically. We used the hypervariable V4 region of the 16S rRNA gene from the 11 species of the genus Herichthys obtained from museum collections to evaluate the existence of phylosymbiosis between the fishes and their gut microbiota. Results The highest diversity values of gut microbiota diversity were found in the detritivorous species while the herbivorous, molluscivorous, and piscivorous showed the lowest diversity values. Differences in gut microbiota were found between species and trophic guilds, in particular for the sympatric species comparison. The phylosymbiosis test was significant showing that the evolution of the gut microbiota is different in species that arise in allopatric and sympatric conditions. Conclusions The most abundant phyla recovered from the gut microbiota were similar to those previously reported in other studies with cichlids supporting the idea that a gut microbial core is conserved in this group of fishes despite millions of years of evolution. Despite the caveats of working with museum specimens, our results provide evidence that gut microbiota divergence could occur even in sympatric conditions and reveals the potential use of museum collections in gut microbiota studies.