Endemic subspecies and multiple stocks have been proposed for spinner (Stenella longirostris) and spotted dolphins (Stenella attenuata), two species with historically high mortality due to bycatch in the eastern tropical Pacific yellowfin tuna fishery. However, there has been low statistical power in tests for genetic differentiation among most of these stocks, due to large historical abundances, ongoing gene flow, and recent divergence. We tested for structure at multiple hierarchical levels by collecting whole mitochondrial genome sequences (mtDNA) and nuclear SNPs (nuDNA) from 104 spinner and 76 spotted dolphins using capture array library enrichment and highly paralleled DNA sequencing. MtDNA showed weak but significant differences between subspecies of spotted (FST: 0.0125; P = 0.0402) and spinner dolphins (FST: 0.0133; P = 0.034). NuDNA supported subspecies of spotted but not spinner dolphins. Relatively strong and significant differentiation was detected between whitebelly and eastern spinner stocks using nuDNA (FST: 0.0297; P = 0.0059). Neither mtDNA nor nuDNA supported the division of existing offshore stocks of spotted dolphins or Tres Marias spinner dolphins. This work identifies a genetic basis for biologically meaningful management units of these two species, a critical component in understanding their response in the face of historical and continued fishery interactions.