The effective population size (Ne) is a crucial characteristic of numerically small populations, positively correlated with their ability to persist in a changing environment and to evolve. Information about the lower bounds of Ne of natural populations is both theoretically interesting and practically important. We studied Kildin cod, an isolated population of Atlantic cod Gadus morhua from an ecologically marginal habitat (marine lake), comparing it with the parental Barents Sea population by a set of 20 microsatellite and protein loci. Overall, the genetic variability in Kildin cod was low (mean allelic richness and heterozygosity: Kildin cod 1.6, 0.26; marine cod 11.6, 0.73). We detected a single locus, the glucose-6-phosphate isomerase-1, which demonstrated a unique variation in the lake. At this locus, about 75 % of the lacustrine fishes carried an allele not found in the sea. The obtained genetic estimates of Ne of Kildin cod (less than a hundred) were much smaller than what is considered as the smalle