Conspicuous male sexual traits (e.g. weapons for male–male competition and displays for courting females) may attract predators. Under conditions of high predation risk, females typically become less choosy with respect to mates to reduce the time spent on mate selection. However, post-copulatory sexual traits, such as sperm ejaculation for sperm competition and sperm removal for cryptic female choice (CFC), may increase with predation risk because they are more inconspicuous to predators. To examine this hypothesis, we observed the reproductive behaviour in the Japanese pygmy squid, Idiosepius paradoxus, in which the male attaches ejaculated spermatangia to the female’s body and the female removes the spermatangia after copulation. Squid from two populations (Ohmura and Oki), with low and high predation levels, respectively, were copulated in tanks under controlled presence/absence of predator conditions. Among the Ohmura individuals, spermatangia removal was suppressed in the presence of a predator. Females may not be able to remove spermatangia effectively when facing a predator because they feel threatened by the predator; as a result, more spermatangia were retained during trials in which they were exposed to predators. In contrast, squid from the Oki (high predation) population, which is exposed to a higher predation risk, were not strongly affected by the predator presence. While the males ejaculated more spermatangia, the females removed more of them. The effect of sexual conflict may be greater than that of the predation risk in the pygmy squid. This suggests adaptive differences in post-copulatory sexual selection traits linked to predation. In general, the strength of pre-copulatory sexual selection decreases with increasing predation risk because the sexual traits attract predators. However, post-copulatory sexual traits which are often inconspicuous may not be influenced by predation risk. Post-copulatory behaviour of Japanese pygmy squid collected from two populations experiencing different predation levels were investigated under experimental predator presence/absence conditions. Among low predations, individual sperm rejection by females (a post-copulatory trait) was suppressed in the presence of a predator. In contrast, individuals from the high predation population reported no change in sperm rejection. As with pre-copulatory sexual selection, post-copulatory female choice was suppressed by predator presence among individuals from a low predation. However, post-copulatory female choice was not affected by predator presence among individuals from the high-predation population. This may indicate predation-driven adaptive differences and plastic responses in post-copulatory traits.