Population genetic structure is widespread in many organisms and can be found at small spatial scales. Population genetic differentiation is an evolutionary precursor to speciation and can have a significant impact on the microevolutionary dynamics of a region. Levels of divergence, in turn, are determined by numerous ecological and evolutionary factors operating on multiple spatial and temporal scales, including spatial heterogeneity, population size and dispersal. My dissertation uses microsatellite markers to investigate the population genetic structure of three vertebrate species that coexist on a common landscape and share ecological predator-prey and competition interactions. I then identify ecological and evolutionary processes important in shaping the observed patterns within a comparative framework. Finally, I explore evolutionary processes that shape adaptive divergence in one of the species, by comparing levels of population differentiation at quantitative traits and neutral molecular markers among ecotypes.