Lactylation has recently emerged as a novel post-translational modification with critical implications for gene regulation and host–parasite interactions, as demonstrated in species of Plasmodium and Trypanosoma. Here, we applied an integrative approach combining in-silico predictive and experimental analyses to detect protein lactylation in parasitic cnidarians in the class Myxozoa. In-silico analyses were conducted using data from seven myxozoan species, six obtained from public databases and one generated in this study. Experimental validation was based on Oxford Nanopore Technologies (ONT) genome sequencing and Western blotting of Myxobolus macroplasmodialis samples. This integrative approach enabled us to validate the in-silico analysis, to identify conserved lactylation sites in key stress-response proteins (including HSP70 and several metabolic enzymes), and to map electrochemical signatures of lactylation sites in the ONT data for M. macroplasmodialis. Comparative analyses across species, supported by functional enrichment and network-based approaches, demonstrated conserved regulatory roles of lactylation alongside species-specific variation in the biological processes it controls. Functional enrichment analyses further implicated lactylation in critical pathways, including glycolysis, oxidative phosphorylation, and immune signaling, supporting its integration into core regulatory networks underlying the functional biology of parasitism.