In species with internal fertilization, females can ‘cryptically’ choose (e.g. through sperm selection) which individuals sire their offspring, even when their overt preferences for copulatory partners are overrun by male–male competition and sexual coercion. The experiment presented here reveals that control of paternity after copulation has begun is also possible in species with external fertilization. Females of the hybridogenetic Rana lessonae–Rana esculenta (LL–LR) waterfrog complex adjust their clutch size in response to mate type: they release fewer eggs when amplexed by hybrid LR males (who jeopardize successful reproduction) than when amplexed by parental LL males. This reduction in the number of eggs laid can increase a female's residual reproductive value through a second mating in the same breeding season or a larger clutch size in the next year. We argue that cryptic female choice through clutch size adjustment (i) may have evolved more often than previously assumed, and (ii) can arise even where females mate only once during a reproductive period.