As the world climate and population levels evolve, high demands are placed on livestock production systems. Small ruminants, especially goats, are critical to the small-scale producer as they are easy to acquire and maintain in sparse pasture and marginal crop regions that cannot easily sustain other livestock. Current small ruminant production systems around the world depend heavily on locally adapted breeds. While indigenous small ruminant genetics are relatively uncharacterized, most have undergone generations of adaptation and genetic isolation or bottlenecks, creating a large genetic reservoir of variation in genes and genetic markers. Identifying genes and genetic markers associated with disease susceptibility and resistance in locally adapted breeds is necessary to preserve local germplasm and to apply state-of-the-art genomic-based strategies to meet global food security challenges. Of particular interest are the genes or genetic markers involved in resistance to internal parasites and disease, and resilience to climate differences. The aim of the current small ruminant genetics and genomics research is the development and utilization of state-of-the-art genomic-based evaluation tools for characterization of sheep and goat populations, development of sustainable strategies for improved production, and increased education and research opportunities. International collaborations have led to the development of de novo genome assembly projects, Illumina SNP panels and, for goats, a collaborative database for submission and access to goat SNP and re-sequencing data for breeds and populations worldwide (ADAPTmap). These tools establish the baseline necessary for the development and application of marker-based selection to the sheep and goat industry.