The octopus fishery in the southern tip of South America is based on Enteroctopus megalocyathus. It is fished on both the Atlantic and Pacific coasts, but no study has yet investigated the genetic variability of this octopus, which is frequently collected as bycatch. The genetic identity and diversity of E. megalocyathus from specimens caught by the king crab fishery along the Beagle Channel in southern Chile was investigated using sequences of three mitochondrial (16S rRNA, COI and COIII) and one nuclear (rhodopsin) markers. Homologous sequences from other Enteroctopodidae were included to determine the genetic variability of E. megalocyathus. In addition to E. megalocyathus, genetic data allowed us to identify Muusoctopus eureka, a species also collected by the king crab fishery. Enteroctopus megalocyathus was found to be genetically similar to E. zealandicus; the genetic distances between these two species were low, 0% (16S rRNA), 0.2% (COI) and 0.6% (COIII), which was also confirmed by the phylogenetic topologies, as both species are in the same clade. Enteroctopus megalocyathus has low levels of genetic diversity, as shown by haplotype and nucleotide diversity values for the mitochondrial markers (Hd = 0.06–0.32; π = 0.0001–0.003), and null diversity for the nuclear marker. All the haplotypic networks resolved with the mtDNA markers showed shared haplotypes among E. megalocyathus, E. magnificus and E. zealandicus. The low genetic diversity of E. megalocyathus can be attributed to both the geological history of South America and the life history of the species, rather than to the king crab fishery.