I combined long-term ecological data and population genetic data using microsatellite DNA markers to examine among- and within-population genetic structure and parentage in Tiger Rattlesnake (Crotalus tigris) populations from the Tucson Basin of southern Arizona located in the northern Sonoran Desert. Based on long-term data from radio telemetry, I determined that C. tigris show strong fidelity to both their home range and winter shelter sites, remaining in close proximity to rocky habitats within mountain ranges, which leads to apparent natural isolation of populations. Therefore, I predicted that C. tigris populations would show substantial genetic differentiation among mountain ranges. However, Bayesian clustering analyses revealed a surprising pattern of extensive admixture among mountain ranges, indicating the presence of gene flow among populations. This pattern of genetic admixture can likely be explained by historical changes in climate and physiognomy in the Sonoran Desert. Analyses of pack rat midden remains clearly show that mountain ranges were previously connected by mesic woodland habitats that may have led to panmixia in C. tigris populations as recently as 5,000-8,000 years ago. At present, C. tigris show a strong preference for xeroriparian washes, which allows individuals to occasionally move relatively long distances, likely resulting in contemporary gene flow. To maintain connections among mountain ranges, I recommend effective management, protection, and restoration (if needed) of wash habitats, which also act as corridors for a suite of other species. At the within population scale, genetic clustering analyses revealed the existence of fine-scale genetic structure in C. tigris subpopulations located in the Rincon Mountains. Further analyses based on location data of individuals indicated the existence of a potential barrier to gene flow, which corresponded to a watershed divide. Although the watershed divide would appear not to present a physical barrier to gene flow, it likely acts to segregate populations based on habitat and movement preferences associated with wash habitats. Data on spatial ecology and reproductive behavior, indicate that C. tigris distribute gametes across the landscape in the absence of actual displacement of individuals due to fidelity to home ranges and winter shelter sites. Analyses of parentage were constrained by the difficulty in obtaining offspring from gravid female C. tigris that give birth deep in rock outcrops. However, I did conduct analyses on over 30 offspring from known mothers and nearly 60 free-ranging offspring found while conducting ecological research. Surprisingly, not a single male C. tigris found courting or copulating with a female was identified as the father, indicating that reproductive behavior is a poor predictor of parentage, and therefore, fitness. Interestingly, males identified as fathers were found up to 2 km distance from their offspring, demonstrating that males from surrounding areas may move relatively long distances to mate. The mating system of C. tigris, which is characterized by promiscuity in both sexes, appears to drive dramatic differences in spatial ecology between males and females, and may lead to fine-scale genetic structure among females and not males who spend a great deal of time searching for receptive females.