This study reports the presence of Kudoa neothunni in yellowfin tuna (Thunnus albacares) landed in Portugal. The parasite was detected in fish harvested from the Indian and Pacific Oceans but not in the Atlantic Ocean specimens. Muscle samples collected from specimens were examined macroscopically and microscopically for parasitic infections. While no Kudoa cysts were observed macroscopically, microscopic analysis revealed K. neothunni in 10 fish (5 each from the Pacific and Indian Oceans), with a prevalence of 20.8% and 20%, respectively. Histological examinations confirmed the presence of Kudoa cysts in infected muscle tissue. Morphological analyses showed stellate spores with 6 polar capsules, and significant differences in spore length and polar capsule dimensions were found between isolates from the 2 oceanic regions. However, phylogenetic analysis based on small and large ribosomal subunit sequences indicated that both spores were consistent with K. neothunni and showed high (100%) similarity to previously published GenBank sequences. These results contribute to the current knowledge of K. neothunni occurrence in yellowfin tuna and indicate that infected specimens originating from the Indian and Pacific Oceans enter the European seafood market. Given that some Kudoa infections can induce post-mortem myoliquefaction and adversely affect fillet quality, this should be considered a potential concern.