In this study we analyzed at a submeso-geographic scale (2 km) the genetic diversity of two sub-populations of Platynereis dumerilii and correlated this with the physical characteristics of the marine currents along the western Black Sea coast. For this purpose, we developed a set of 13 new polymorphic microsatellite markers and used them to assess the genetic differentiation, as well as the bi-directional migration rates between the studied sub-populations. We also computed the Peclet number (Pe) as an indicator of the relative effect of advection and eddy diffusion on larval dispersion for the specific conditions of the Black Sea study area. The results indicated no genetic structure in P. dumerilii sub-populations which indicates that the longitudinal alongshore currents dominate in the population structuring of this species. This finding is important, because with the average current speeds of 5 cm/sec on the Black Sea coast during May–August we might have expected a certain population structuring to occur. In accordance with the periodical change of direction of the longitudinal current (either form North to South, or form South to North) the gene flow was found to be bi-directional, with the same intensity. J. Exp. Zool. 321A: 41–47, 2014. © 2013 Wiley Periodicals, Inc.