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Females control the paternity of their offspring by selectively mating with males they perceive to be of high quality. In species where females mate with multiple males in succession, females may bias offspring paternity by favoring the sperm of one male over another, a process known as cryptic female choice. 1 While evidence of cryptic female choice exists in multiple taxa, the mechanisms underlying this process have remained difficult to unravel. 2 Understanding cryptic female choice requires demonstration of a female-driven post-mating bias in sperm use and paternity and a causal link between this bias and male cues. 3 In this study, we present evidence of cryptic female choice in female Drosophila melanogaster. Through experiments utilizing transgenic males expressing fluorescent sperm, we observed that exposure to attractive males between matings prompts females to expel the ejaculate of their initial mate more rapidly than in the presence of less attractive males. While doing so, females exhibit a bias in sperm storage against their first mate, thereby favoring the paternity of their subsequent mate. Our findings reveal that females adjust the timing of ejaculate expulsion in response to male pheromones in their environment, specifically heptanal and 11- cis -vaccenyl acetate, which are sensed by females through specific odorant receptors. We provide a cryptic female choice mechanism allowing a female to modulate the share of paternity of her first mate depending on the sensing of the quality of potential mates in her environment. These findings showcase that paternity can be influenced by events beyond copulation. [Display omitted] • D. melanogaster females exert cryptic mate choice • Females eject their first mate's ejaculate faster in the presence of attractive males • Females exposed to attractive males bias sperm storage against their first mate • Male pheromones heptanal and cVA are sufficient to shorten ejection latency Doubovetzky et al. present evidence of cryptic female choice in Drosophila melanogaster. Females exposed to pheromones of attractive males expedite ejaculate ejection from their first mate, favoring subsequent mates' sperm. This work highlights that female fruit flies can influence paternity of their offspring through post-copulatory mechanisms. [ABSTRACT FROM AUTHOR]