Habitat fragmentation can restrict the dispersal of individuals from one population to another, which often results in the loss of genetic diversity due to reduced gene flow, inbreeding, and genetic drift. The stability and long-term survival of animal populations in fragmented landscapes largely depends on their ability to disperse among patches. The main goal of this dissertation is to evaluate how human-modified heterogeneous landscapes impact population structure, dispersal, and gene flow of the silvery brown tamarin (Saguinus leucopus), an endangered and endemic primate of Colombia. In this study I use a multidisciplinary approach and combine genomic data with spatial analysis and ecological modeling to determine how anthropogenic and natural landscape features shape tamarin genetic variation. I describe a cost-effective reduced representation method called ddRAD-seq developed to identify and genotype large numbers of genome-wide SNP loci for taxa from across the New World monkeys. I test the utility of this approach to resolve platyrrhine evolutionary relationships at different time scales and discuss the protocol's promise in molecular primatology. Using this method, I investigate population structure across the S. leucopus distribution. Using traditional and novel population genetic approaches, I detect population structure between geographic regions at different hierarchical levels and find population structure to be associated with geographic distance. In addition, using individual-based landscape genetic analyses in combination with spatial and ecological modeling, I also found that anthropogenic and natural landscape features - beyond simple Euclidean distance - have an effect on the genetic relationships and population structure of the silvery brown tamarin. Remnants of secondary forest in an agricultural matrix and water bodies represent moderate barriers to tamarin gene flow and have a significant effect on genetic relationships and population structure of the silvery brown tamarin. Lastly, I assess structural and functional connectivity throughout the silvery brown tamarin's distribution using least-cost paths and circuit theory. I identify potential patches of tamarin habitat and prioritize patches and corridors important in maintaining landscape connectivity. I discuss the conservation implications of these results and offer recommendations and management guidelines for conservation authorities regarding the conservation and management of S. leucopus populations in a human-dominated landscape.