ABSTRACT The eukaryome of mammals contains parabasalid protists that dramatically affect host immune function and health. However, the prevalence and diversity of parabasalids in wild reptiles and the consequences of captivity on these symbiotic protists are unknown. Reptiles are ectothermic, which expose their microbiomes to temperature fluctuations such as those driven by climate change. Thus, conservation efforts for threatened reptile species may benefit from understanding how shifts in temperature and captive breeding influence the microbiota, including parabasalids, to impact host fitness and disease susceptibility. Here, we surveyed intestinal parabasalids in wild reptiles from across three continents and compared these to captive animals. Reptiles harbor surprisingly few species of parabasalids compared to mammals, but these protists exhibited a flexible host range, suggesting specific adaptations to reptilian social structures and microbiota transmission. Furthermore, reptile-associated parabasalids are adapted to wide temperature ranges and survive colder temperatures significantly better than human-associated parabasalids. Colder temperatures altered the protist transcriptomes, causing increased expression of genes associated with detrimental interactions with their hosts. Our findings establish that parabasalids are widely distributed in the microbiota of both wild and captive reptiles and highlight how these protists respond to temperature fluctuations encountered in their ectothermic hosts. IMPORTANCE Environmental factors like climate change and captive breeding can impact the gut microbiota and host health. Therefore, conservation efforts for threatened species may benefit from understanding how these factors influence animal microbiomes. Parabasalid protists are members of the mammalian microbiota that can modulate the immune system and impact susceptibility to infections. However, little is known about parabasalids in reptiles. Here, we profile reptile-associated parabasalids in wild and captive reptiles and find that captivity has minimal impact on parabasalid prevalence or diversity. However, because reptiles are cold-blooded (ectothermic), their microbiotas experience wider temperature fluctuation than microbes in warm-blooded animals. To investigate whether extreme weather patterns affect parabasalid-host interactions, we analyzed the gene expression in reptile-associated parabasalids and found that temperature differences significantly alter genes associated with host health. These results expand our understanding of parabasalids in this vulnerable vertebrate group and highlight important factors to be taken into consideration for conservation efforts.