Female eumetazoans often develop sperm storage organs (SSOs). Although the processes of sperm storage may influence post-copulatory sexual selection in polyandrous species, the significance of multiple SSOs is not understood. In contrast to coastal squids (which develop no more than two SSOs), the female Todarodes pacificus, a more oceanic species, develops more than 20 SSOs, which take the form of specialized pockets, called seminal receptacles (SRs), near the mouth. We investigated the sperm storage pattern of SRs by paternity analysis of hatchlings obtained after artificial insemination using sperm retrieved from 6 arbitrarily selected SRs. The results showed that females were capable of storing sperm contributed by 9 to 23 males, indicating that females are broadly promiscuous. In the pattern of sperm storage, the number of males and proportion of their sperm present in the SRs varied among SRs, and sperm storage was biased towards particular males at the individual SR level. However, when calculated as a proportion of all the SRs within a female, the number of sires increased and the paternity bias towards any particular male weakened. These results suggest that one function of having multiple SRs in T. pacificus may be to ensure genetic diversity of the offspring.