Two sympatric sibling Polydora species, P. cf. ciliata (Johnston) boring into calcareous substrata and P. limicola Annenkova inhabiting mud tubes in fouling on bottoms of ships, were investigated through their allozyme variations by means of starch gel electrophoresis. A survey of 18 enzyme systems comprising 27 loci showed a lack of common alleles at 10 loci: Fdh, Fum, Got-2, Gpi-1, Gpt, Lap, Mdh-1, Mdh-2, Sdh, Sod and duplication of alkaline phosphatase gene in P cf. ciliata and glucose phosphate isomerase gene in P limicola. Our genetic data indicate that we have two good congeneric Polydora species distinguishable by their allozyme variation and different in their ecology. The values of Nei's indices of genetic identity and standard genetic distance between the two species are I = 0.317 and D = 1.149. At the same time, the long-standing systematic ciliata-limicola problem remains unsolved and requires further investigations because the well-known ''boring'' species, P. ciliata was first described as living in fine, soft mud.