Data sets used to support analysis published by O'Corry-Crowe et al (2014) Crossing to safety: Dispersal, colonization and mate choice in evolutionarily distinct populations of Steller sea lions, Eumetopias jubatus. Molecular Ecology 23(22): 5415-5434. Data include Steller sea lion genetic data obtained from samples collected from pups on natal rookeries. The genetic data are genotypes at 16 microsatellite loci and haplotypes at mtDNA, spatial data, and allelic and haplotypic frequencies.