Species-genetic diversity correlations (SGDCs) are useful indicators of processes that simultaneously affect diversity at multiple biological levels. We combined spatial and temporal sampling of 4 study sites in the Danish Isefjord-Roskilde Fjord Estuary at 4 time points over 1 yr to investigate the effect of seasonal variation on SGDCs. Species diversity was estimated as species richness from samples comprising 20752 individuals representing 51 benthic invertebrate taxa. Genetic diversity was estimated for a single focal taxon, the polychaete Pygospio elegans, as mean allelic richness at 7 microsatellite loci. Combining all samples, a significant positive correlation between species richness and allelic richness was found. Median sediment grain size and mean temperature had significant effects on species richness, whereas only mean temperature had a significant effect on allelic richness of P. elegans. Our results show that both the benthic community as a whole and populations of P. elegans respond similarly to seasonal environmental variation at the study sites. The results suggest that seasonal timing of reproduction and dispersal in this temperate marine habitat might have a greater influence on diversity than spatially varying environmental variables and highlight the benefits of also investigating temporal SGDCs. Because of seasonal changes in diversity, it is important that samples are compared on the same time scale when investigating SGDCs.