This study investigates the impact of habitat degradation on the gastrointestinal (GI) microbiomes of Mexican black howler monkeys (*Alouatta pigra*). The researchers collected fecal samples from six groups of howlers occupying different habitats, including a continuous evergreen rainforest, an evergreen rainforest fragment, a continuous semi-deciduous forest, and a wildlife center. High-throughput 16S ribosomal RNA gene sequencing revealed that the diversity, richness, and composition of howler GI microbiomes varied with host habitat and diet. Howlers in suboptimal habitats consumed less diverse diets and had less diverse gut microbiomes. Quantitative real-time PCR also showed a reduction in genes related to butyrate production and hydrogen metabolism in these howlers, which may affect their health. The study highlights the importance of understanding the relationship between host habitat, diet, and GI microbiome composition for conservation efforts and the well-being of wild primates.This study investigates the impact of habitat degradation on the gastrointestinal (GI) microbiomes of Mexican black howler monkeys (*Alouatta pigra*). The researchers collected fecal samples from six groups of howlers occupying different habitats, including a continuous evergreen rainforest, an evergreen rainforest fragment, a continuous semi-deciduous forest, and a wildlife center. High-throughput 16S ribosomal RNA gene sequencing revealed that the diversity, richness, and composition of howler GI microbiomes varied with host habitat and diet. Howlers in suboptimal habitats consumed less diverse diets and had less diverse gut microbiomes. Quantitative real-time PCR also showed a reduction in genes related to butyrate production and hydrogen metabolism in these howlers, which may affect their health. The study highlights the importance of understanding the relationship between host habitat, diet, and GI microbiome composition for conservation efforts and the well-being of wild primates.