Temporal sampling within the spring-spawning season has revealed differentiation in length-at-age in herring at Rugen and differentiation in, e.g., Anisakis infestation rate, otolith microstructure, and gillraker counts in Gdansk Bay, leading to the expectation that spawning waves consist of distinct herring populations. We tested this expectation by analysing genetic variation at nine microsatellite loci in samples collected at different times during the March to May spawning season in 2 consecutive years, 2002 and 2003. Length-at-age, mean length, and age distributions were compared among samples within locations but did not show consistent temporal patterns. Pairwise genetic differentiation among temporal samples within season was low and non-significant in the Gdansk Bay (0 <F-ST <0,0025) but higher among Rugen samples (0.0008 <F-ST <0.0113). Samples from Rugen collected in 2002 differed significantly from each other, and individual assignment tests showed increased divergence with time. Differentiation was not confounded by effects of age class or sex. We conclude that spawning waves are not genetically differentiated among Gdansk samples based on factors analysed in this study, whereas genetically distinct but sympatric spawning populations may be found at Rugen. (c) 2005 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved.