Genetic research is a well-recognized component of understanding biodiversity and is an invaluable approach for documenting and mitigating increasingly high rates of loss. Here we present a quantitative synthesis of conservation genetics science in Latin America and its progress, focusing on evolving trends on different taxonomic groups, environments and markers. We reviewed 528 conservation genetics research papers published in 57 journals from 1992 to 2013. Brazil and Mexico were the most represented countries in the literature and there was a marked disparity between terrestrial (~64%) and aquatic-marine research (~36%). More than a third or the articles focused on plants (~35%) while the other (65%) were animal studies with a clear emphasis on mammals (35%) and bony fishes (24%). Most research (42%) addressed patterns of population structure, while 17% focused on genetic diversity issues and 14% focused on the description of novel genetic markers. Finally, although genetics has become an integral part of conservation biology, genetic analyses have often not been completely integrated into the development of conservation and management strategies and formal policies. We discuss the levels to which these types of studies can effectively contribute to biodiversity conservation in this region, and offer suggestions on how conservation genetic approaches may be used more broadly, enhancing the connectivity between scientists and policy makers.