Having been successfully bred in semi-intensive and intensive aquaculture systems, oval squids of the Sepioteuthis lessoniana species complex are emerging as promising candidates for research and industry. Nevertheless, information about pathogens and diseases that may affect squid aquaculture remains sparse. In this study, we identify new parasitic copepod species that causes squid mortality and decreases squid hatching rates, and we also offer a solution to eliminate the pathogen during incubation of squid eggs. The newly discovered copepod Ikanecator primus gen. et sp. nov. was identified on oval squid eggs for the first time using both morphological and molecular diagnostic markers. In the genomes of the copepod and associated microbiome, we identified multiple genes for enzymes involved in cephalopod eggshell degradation in genomes of the copepod and associated microbiome. Furthermore, we conducted experiments to assess efficacy of peracetic acid in inhibiting the I. primus gen. et sp. nov. both in vitro and in vivo using immersion treatment. We established that a 2-min exposure to a concentration of 250 μl/L of peracetic acid containing product (PAA-product; 35 mg/L PAA and 15 mg/L H2O2) inhibited the development of nauplii in vitro. All parasites exposed to a concentration of 500 μl/L of PAA-product (70 mg/L PAA and 30 mg/L H2O2) were eliminated within two minutes. On top of this, the immersion treatment with 500 μl/L of PAA-product (70 mg/L PAA and 30 mg/L H2O2) improved survival of squid embryos and increased size of squid hatchlings compared with control and the immersion treatment with 125 μl/L of PAA-product (17.5 mg/L PAA and 7.5 mg/L H2O2) and the immersion treatment with 250 μl/L of PAA-product (35 mg/L PAA and 15 mg/L H2O2). These findings suggest that PAA holds a great potential as inhibitor and controller of parasitic copepod infections and for overall health management in cephalopod culture.