While links between environmental factors, gut microbiome composition, and host health have been well documented, details of these relationships remain unclear. By analyzing fecal samples from a diverse set of captive non-human primates (NHPs) from a single zoo, we aimed to further explore the ways in which captivity influences the NHP gut microbiome. All samples were processed using both “open” and “closed reference” pipelines. Open reference analysis used DADA2 de novo ASV clustering and both the SILVA and Greengenes databases, while closed reference analysis used only the Greengenes database. Both pipelines returned highly similar results, indicating that they could both be valid ways to process this type of microbiome data, and further supporting our conclusions. Using both methods, we found that within the sampled captive individuals, host species was the clearest driver of microbiome composition. However, when comparing captive and wild individuals from similar species, captivity status had a greater influence on microbiome composition than host species. Additionally, historic antibiotic usage was linked to a pattern of decreased alpha diversity and community evenness in captive emperor tamarins (Saguinus imperator), the species with the most sampled captive individuals. While this study provides novel insights into the gut microbiomes of diverse NHP species, work is ongoing to further investigate the specific impact of individual factors.