Gut microbial communities have critical effects on the homeostasis and disease states of animals. Currently, the most well studied portion of the gut microbiome is the bacteriome, which is the collective taxa of bacteria that inhabit the gut. Health-related outcomes influenced by the gut bacteriome are in part a product of bidirectional communication between bacteria and host via endocrine axes such as the hypothalamo-pituitary adrenal (HPA) and gonadal axes (HPG). Measuring these relationships in wild alloprimates offers a novel method for monitoring the physiological outcomes of ecological interactions with potential evolutionary significance. Herein, we examined interactions across the HPA, HPG, and hypothalamo-pituitary thyroid (HPT) axes, and the fecal bacterial communities of wild mantled howler monkeys (Alouatta palliata) of Barro Colorado Island, Panama. Using fecal samples (n = 88), we measured fecal estrogens (fE), fecal androgens (fT), fecal glucocorticoids (fGCs), and fecal thyroid hormone metabolites (fT3) and sequenced bacterial taxa (n = 55). Bacterial communities were classified from the phylum to amplicon sequence variant (ASV) level. We found that alpha diversity of gut bacteria in female howlers was related to an interaction between fGCs and fE. There was no such interaction with fT. Beta diversity in female howlers was partially explained by fGCs levels and group affiliation. In males, we found that fGCs were inversely correlated with Shannon diversity at the ASV level. Future research should examine these relationships over time, with the goal of exploring how short and long term perturbances influence gut bacteria-hormone relationships in wild and captive animals.