Male genitalia show rapid and divergent evolution. It is rarely determined whether variation in male genital morphology influences male reproductive success. Male damselflies possess a unique aedeagus with a re-curved head and spiny lateral processes, and most females have two sperm storage organs, a spherical bursa copulatrix and a tubular spermatheca. Previous studies have indicated that the re-curved head may remove bursal sperm, whereas the lateral processes remove spermathecal sperm. However, we need more direct evidence of these functions. We compared sperm number in female sperm storage organs by interrupting copulation to examine sperm removal by the male. In Calopteryx cornelia, males removed almost all bursal sperm but only partially removed spermathecal sperm. In contrast, females of Mnais pruinosa store sperm primarily in the bursa, and males removed only bursal sperm. To examine the functions of male spiny lateral processes, we compared mating behaviour between control and experimental males from which we removed (cut) the lateral processes. In C. cornelia, cutting of the lateral processes resulted in a decreased number of abdominal movements during copulation and no removal of spermathecal sperm. The amount of bursal sperm removed during copulation also decreased in experimental males compared to the unmanipulated males. However, in M. pruinosa, the experimental removal of male lateral processes did not decrease the abdominal movements and little affected the removal of bursal sperm. Inter-specific differences between C. cornelia and M. pruinosa may be caused by variation in the strategies of female sperm storage.