The effect of time on genetic differentiation was studied among infrapopulations of mature specimens of the hemiurid fluke, Lecithochirium fusiforme, a parasite of marine fishes. Genetic distances and genetic structure within and among different temporal samples of a geographical population were investigated using starch gel electrophoresis, by screening 6 polymorphic loci in 2 groups of infrapopulations corresponding to different sampling data, i.e., winter 1997–1998 and autumn 1998. The genetic distance among infrapopulations was low (D = 0.000–0.058 ± 0.041). However, genetic divergence among infrapopulations from the same geographic location was clearly lower within each temporal sample (G_ST = 0.021 and 0.034) than the corresponding value obtained for 12 infrapopulations sampled at different seasons of the year (G_ST = 0.067). These results suggest the existence of a relatively important temporal effect that accounts for the differences in genetic variability among adult infrapopulations of L. fusiforme. Therefore, a hypothetical temporal gene flow favored by the existence of persistent life-cycle stages of this species in paratenic hosts is not sufficient to mask the temporal differentiation caused by genetic drift.