To determine the pattern of spatial genetic structure in the endemic Southern Ocean octopus Adelieledone polymorpha, microsatellite loci were isolated from partial genomic libraries enriched for repetitive DNA motifs. Seven dinucleotide and two trinucleotide microsatellite loci were isolated successfully and levels of polymorphism were quantified in 34 individuals sampled from the Southern Ocean near South Georgia. No pairs of microsatellite loci were linked significantly; however, one locus deviated (P < 0.05) from Hardy-Weinberg equilibrium. Overall, the nine loci produced between five and 16 alleles, with observed and expected heterozygosities varying between 0.22 and 0.86 and between 0.21 and 0.94 respectively. This is the first description of microsatellite loci from an octopus endemic to the Southern Ocean, and these genetic markers are being used to quantify spatial structure within A. polymorpha.