Recent studies have shown that the mammal microbiome is modified by environmental conditions, and that reduced microbiome functionality is associated with host health issues. Microbiome data in wild and captive primate populations can therefore be used to assess their health as they encounter a variety of environments. Comparative studies of the microbiome can also inform disease ecology, conservation, and captive management strategies tailored to different primate species. Therefore, this study examines how the hair, oral, and gut microbiota of nine wild and captive lemur species are determined by host phylogenetic relationships and host environment. I found that host species identity appeared to explain most of the variation in microbiome composition: lemurs in the same genus had similar microbiomes, even across different environments. Surprisingly, lemurs living in both low and high disturbance areas in the wild had less diverse microbiomes than captive lemurs, adding to the growing body of evidence that microbiome diversity may not be a consistent indicator of microbiome health. Instead, microbiome composition and differential abundance of microbes across samples may reveal more about meaningful shifts in the microbiome. Wild lemur microbiomes varied more in composition than captive lemur microbiomes, which were all similar and less variable even across different captive institutions. This suggests that captivity has a Westernizing and homogenizing effect on the microbiome. This effect was more strongly observed in the gut and hair microbiome than the oral microbiome. Based on the results of this study, the oral microbiome appears to be a conserved and highly filtered microbial community. Conversely, the hair microbiome is most subject to external effects and can serve as an indicator of the environmental microbes to which the host is exposed. The effect of host environment on the microbiome was also more strongly observed in folivorous lemurs (Propithecus spp.) compared to the other generalist and frugivorous lemurs in the study, which aligns with previous research which found that folivore microbiomes are more strongly affected by captivity and habitat disturbance. This project is the most comprehensive comparative full-body analysis of the lemur microbiome to date.