We isolated and characterized 13 novel microsatellite loci using reduced representation genomic DNA sequences from a single (Somniosus microcephalus) individual. Of the 50 microsatellite loci screened in 36 individuals, 24 successfully amplified through PCR. Of those loci, 11 proved to be monomorphic or produced multiple peaks in fragment length analysis through capillary electrophoresis. The remaining 13 loci produced between 2 and 9 alleles, and observed and expected heterozygosity ranging from 0.063 to 0.750 and 0.117 to 0.770, respectively.