Recently, oval squid of Sepioteuthis lessoniana species complex has gained importance in aquaculture due to its successful breeding in semi-intensive and intensive aquaculture systems. However, there is a lack of information regarding pathogens and diseases that can affect this species, prompting the need for further research. Two cestode species, Nybelinia enterika sp. nov. and Phoreiobothrium sp., were identified as members of the Trypanorhyncha and Onchoproteocephalidea orders, respectively, using both morphological and molecular diagnostic markers in wild-caught oval squids (Sepioteuthis lessoniana sp.1, S. lessoniana sp.2, S. lessoniana sp.3). These cestode species were found to use the oval squids as intermediate hosts. In histopathology samples, the infected squid with N. enterika was surrounded by numerous hemocytes in the infected area. In the genomes of both cestode species, we identified multiple genes for enzymes involved in cephalopod tissue degradation, such as cysteine proteases including cathepsin-L, cathepsin-D, cathepsin-A, cathepsin-B, cathepsin-K, and cathepsin-S. These enzymes potentially help the parasites manipulate the squid immune system and neutralize squid hemocytes. The detection of these parasites in wild squid populations, with 100% prevalence in Okinawa, is concerning as the effect of these parasites on human consumers' health remains unknown. However, our research demonstrated that fully cultured squid remain completely cestode parasite-free, indicating they are more likely to meet the highest standards for food safety and quality.