According to a recent demographic survey, the population structure of Pectinaria koreni might fit a source–sink metapopulation model at least at a regional scale. Spatial and temporal genetic structure of the populations present in the Baie de Seine (eastern Baie de Seine and Baie des Veys) was assessed using four highly polymorphic microsatellite loci which have revealed strong intra-locality genetic diversity. In the eastern Baie de Seine, both temporal (1994–1996) and spatial (1994) genetic differentiation were relatively low but significantly different from zero despite a 15-day dispersing larval stage. Such structures may be explained by the settlement of larvae from different gene pools and differing recruitment histories among sites within the eastern Baie de Seine. At a larger scale, similar levels of spatial differentiation were observed in 1999 between the eastern Baie de Seine and the Baie des Veys. The lack of any significant differences in gene diversity and allelic richness rules out a source–sink functioning at the scale of our study. The present paper provides further knowledge on the population dynamics of a univoltine species and its persistence in a highly dispersive environment via a shifting spatial mosaic.