The arginine vasopressin (AVP) and oxytocin (OT) hormone pathways are involved in a multitude of physiological processes, and their receptor genes (AVPR1A and OXTR) have been implicated in increased partner preference and pair bonding behavior in mammalian lineages. This observation is of considerable importance for understanding social monogamy in primates, which is present in only a small subset of primate taxa, including Azara's owl monkeys (Aotus azarai). Thus, it is the goal of this dissertation to examine the molecular evolution of AVPR1A and OXTR in owl monkeys to better understand how the pro-social behaviors related to those loci may have evolved. However, in order to properly contextualize functional neurogenetic variation related to such sociobehavioral pattterns, it is necessary to first establish the range of molecular variation occurring at non-related genetic loci. To address this issue, we sequenced the entire mitochondrial genome of two species of Aotus (A. azarai and A. nancymaae), and analyzed 39 haplotypes of the mitochondrial COII gene from ten different owl monkey taxa. Next, to understand the recent evolutionary history and genetic structure of our focal owl monkey population, we assessed variation of the mtDNA control region (D-loop) in 118 wild individuals. Furthermore, to establish our knowledge of genetic kinship and individual identity within the wild population, we investigated autosomal variation in the form of 24 short tandem repeat (STR) microsatellite loci. In concert with these analyses, we characterized the molecular features of AVPR1A and OXTR in A. azarai and other platyrrhines through direct sequencing, and demonstrated that there are substantial sequence differences at both loci across primate species. These data provide new clues on the possible basis of pair bonding in New World species, and may help to explain the sporadic appearance of monogamy in this infraorder. Specifically, despite a common molecular origin, we argue that the AVP and OT pathways have evolved in markedly different ways, due in part to their chromosomal locations and their relative proximity to regions of molecular instability. This study reinforces the notion that neurogenetic loci in primates have undergone significant evolutionary changes, and suggests that monogamy has arisen multiple times in the primate order through different molecular mechanisms.