Habitat degradation impacts the gastrointestinal (GI) microbiomes of black howler monkeys (Alouatta pigra). This study compared the GI microbiomes of six groups of black howler monkeys inhabiting different habitats, including a continuous evergreen rainforest, a rainforest fragment, a continuous semi-deciduous forest, and captivity. High-throughput 16S rRNA gene sequencing showed that the diversity, richness, and composition of the GI microbiomes varied with host habitat, related to diet. Howlers in suboptimal habitats had less diverse diets and consequently less diverse gut microbiomes. Quantitative real-time PCR revealed reduced genes related to butyrate production and hydrogen metabolism in suboptimal habitats, which may affect host health. The study found that howlers in the continuous evergreen rainforest had the most diverse and rich GI microbiomes, while captive and fragmented habitat howlers had less diverse microbiomes. The microbiome composition was dominated by Firmicutes and Bacteroidetes, with variations in the abundance of specific genera depending on habitat. Captive howlers had higher levels of Proteobacteria and Succinivibrio, while FR howlers had higher levels of Verrucomicrobia. The GI microbiome composition was also influenced by diet, with howlers in different habitats showing distinct microbial profiles. Dietary shifts were associated with changes in the GI microbiome composition, with howlers in the rainforest consuming more diverse diets and having more varied microbiomes. The study also found that habitat degradation may lead to dysbiosis, characterized by reduced microbial richness and diversity, which could negatively affect host nutrition and health. The GI microbiome plays a critical role in energy metabolism, particularly through the production of short-chain fatty acids like butyrate, which supports intestinal health. However, in degraded habitats, the microbiome may be less efficient, more susceptible to pathogenic invasion, and less resilient to disturbances. The study highlights the importance of understanding the relationship between host habitat, diet, and GI microbiome composition for conservation efforts. Habitat degradation may negatively impact the health of black howler monkeys by altering their GI microbiomes, which in turn affects their nutrition and overall well-being. The findings suggest that conservation strategies should consider the impact of habitat degradation on the GI microbiome and the potential consequences for primate health.Habitat degradation impacts the gastrointestinal (GI) microbiomes of black howler monkeys (Alouatta pigra). This study compared the GI microbiomes of six groups of black howler monkeys inhabiting different habitats, including a continuous evergreen rainforest, a rainforest fragment, a continuous semi-deciduous forest, and captivity. High-throughput 16S rRNA gene sequencing showed that the diversity, richness, and composition of the GI microbiomes varied with host habitat, related to diet. Howlers in suboptimal habitats had less diverse diets and consequently less diverse gut microbiomes. Quantitative real-time PCR revealed reduced genes related to butyrate production and hydrogen metabolism in suboptimal habitats, which may affect host health. The study found that howlers in the continuous evergreen rainforest had the most diverse and rich GI microbiomes, while captive and fragmented habitat howlers had less diverse microbiomes. The microbiome composition was dominated by Firmicutes and Bacteroidetes, with variations in the abundance of specific genera depending on habitat. Captive howlers had higher levels of Proteobacteria and Succinivibrio, while FR howlers had higher levels of Verrucomicrobia. The GI microbiome composition was also influenced by diet, with howlers in different habitats showing distinct microbial profiles. Dietary shifts were associated with changes in the GI microbiome composition, with howlers in the rainforest consuming more diverse diets and having more varied microbiomes. The study also found that habitat degradation may lead to dysbiosis, characterized by reduced microbial richness and diversity, which could negatively affect host nutrition and health. The GI microbiome plays a critical role in energy metabolism, particularly through the production of short-chain fatty acids like butyrate, which supports intestinal health. However, in degraded habitats, the microbiome may be less efficient, more susceptible to pathogenic invasion, and less resilient to disturbances. The study highlights the importance of understanding the relationship between host habitat, diet, and GI microbiome composition for conservation efforts. Habitat degradation may negatively impact the health of black howler monkeys by altering their GI microbiomes, which in turn affects their nutrition and overall well-being. The findings suggest that conservation strategies should consider the impact of habitat degradation on the GI microbiome and the potential consequences for primate health.