Electrophoretic analysis of 10 protein systems in each of eight species of deep sea (1,000-2,000 m) invertebrates from the Atlantic and Pacific Oceans yields a liberal estimate of 47% and a conservative estimate of 30% polymorphic loci out of 74 loci surveyed. These figures typify estimates for organisms inhabiting heterogeneous terrestrial and aquatic environments and do not support the hypothesis that the fauna of this very stable environment is genetically impoverished. Three hypotheses accounting for the high level of genetic variability are discussed: (1) the neutrality of alleles, (2) physiological heterosis, and (3) diversifying selection operating over a pressure gradient.