Kudoa barracudai n. sp. has been found infecting the muscles of Sphyraena putnamae from Red Sea, Saudi Arabia. The prevalence of the infection was 10 % (5/50). Its ovoidal plasmodia encapsulated with fibrous connective tissue and measuring 700 × 510 μm. Local myolysis was observed around the plasmodia without inflammatory reaction. Mature spores were quadrate in the apical view with rounded edges and subspherical to ovoid in the side view and measured 5 μm (4.5-5.5) in width and 5.5 μm (5-6) in thickness. Polar capsules were pyriform, equal in size, and measured 2.5 μm (2-3) in length and 1.5 μm (1-2) in width with two filament coils. Ultrastructural analysis showed a demarcated border between the parasite cellular mass and host cellular components that represented the cyst wall, and cysts were filled with mostly mature spores. Phylogenetic analysis of the small subunit ribosomal RNA (SSU rRNA) using the maximum likelihood and Bayesian inference approaches showed the new species clustered in a robust clade with Kudoa amamiensis, Kudoa kenti, and Kudoa quraishii. The SSU rRNA gene of K. barracudai was most similar to K. amamiensis (98.7 %), followed by K. kenti (97.4 %) and K. quraishii (96.6 %). This combination of morphological data and molecular analysis served to identify this parasite as a new species of Kudoa, which we have named K. barracudai n. sp.