Previous studies have identified several factors that shape the microbiome of a host, such as diet, gut anatomy, host phylogeny, reproductive stage, season, altitude, and geography. In this study we focus on two of these factors—geography and host We characterize the fecal microbiota of the endangered Big-headed Turtle (Platysternon megacephalum) and compare across a relatively fine geographic scale (3 populations within an 8-km radius). We found the fecal microbiota to vary between the most distant sites, and infer the difference to be due to food availability, environmental microbiota,or both. For host, we compare the fecal microbiota of individuals of P. megacephalum and the Beale’s Eyed Turtle (Sacalia bealei) that are syntopic. The fecal microbiota differs between these two host species, and may be due to diet and/or host-adapted bacteria. Since these individuals were collected from the same place at the same time, differences in environmental microbiota likely have little to no effect. We encourage more researchers to collect gut microbiota data of wild turtles, so we can better understand and apply microbiota data to conservation.