The cuttlefish Sepia pharaonis species complex is emerging as a promising set of organisms for research in neuroscience, the behavioral sciences, and commercial aquaculture. At the same time, information about pathogens and diseases that could affect cuttlefish cultivation in intensive aquaculture settings remains limited. Our study has identified two species of parasite, the protozoan Liburna oophaga sp. nov. and the metazoan Ikanecator primus, that co-infect cuttlefish eggs, increasing mortality and reducing hatching rates. L. oophaga sp. nov. is reported here for the first time to enhance mortality during the incubation period by inducing deformity in cuttlefish eggs. We investigated the application of peracetic acid to parasite elimination during cuttlefish egg incubation. When cuttlefish eggs were treated with a peracetic acid containing product (PAA-product); 35 mg/L PAA + 15 mg/L H 2 O 2 , L. oophaga on the surfaces of the eggs were eliminated within 10 min. PAA-product; 70 mg/L PAA + 30 mg/L H 2 O 2 was required to achieve the same effect for I. primus. Immersion treatment with PAA-product at 70 mg/L PAA + 30 mg/L H 2 O 2 reduced parasitic load and improved survival of cuttlefish embryos and hatchling size, demonstrating that PAA product can inhibit and control parasitic co-infections in cephalopod culture.