Complex ecological interactions or physiological adaptations increasing immunity may limit parasite establishment in some host populations. The Madrean Sky Islands are regarded as a series of complex ecological systems rife with speciation and biodiversity. These desert ecosystems are subject to extreme abiotic fluctuation. The Sonoran mud turtle (Kinosternon sonoriense) is one of the only semi-aquatic turtle species capable of surviving in these habitats. Fecal analysis (n=217), blood smears (n=18), and dissection (n=4) were utilized to characterize the interpopulational variation in parasite prevalence among three closely-related Kinosternid species. These species occupy environments along a gradient with varying degrees of hydration and aquatic permanence. Kinosternon sonoriense populations occupying extreme habitats within the Madrean Sky Islands had a significantly lower parasite prevalence than yellow mud turtle (Kinosternon flavescens) populations (p = < 0.001, 95% CI [14.688, 153.306]) and eastern mud turtle (Kinosternon subrubrum) populations (p = 0.04762, 95% CI [0.814, 15.598]). White blood cell estimates among species were also significantly different (df= 2, p = < 0.05) providing further evidence that Kinosternon flavescens and Kinosternon subrubrum harbor larger parasite communities than Kinosternon sonoriense populations. Necropsy of Kinosternon sonoriense yielded no evidence of parasitism or pathology. Differential habitat use as well as the extreme environment itself likely contributes to these differences. However, further study should be conducted on parasite-host interactions in extreme environments to better understand the ecological mechanisms preventing parasite establishment in the Madrean Sky Islands. Understanding the ecology of Kinosternon sonoriense and the utilization of ephemeral aquatic habitats will aid in future conservation efforts in the Southwestern United States.