Myxozoans are a diverse group of parasitic cnidarians of wide distribution. A new species, Myxobolus matogrossoensis n. sp., is herein described infecting wild specimens of tetra mato-grosso Hyphessobrycon eques, caught in the Pantanal biome, the world’s largest tropical wetland area. Cysts were found in 3 of the 30 examined fishes. Mature myxospores were ovoid in shape in frontal and measured 6.6 ± 0.4 µm (6.2–7.0 µm) in length and 3.5 ± 0.2 µm (3.3–3.7 µm) in width. The two polar capsules were elongated in shape, equal in size and occupying almost half of the myxospore body. They measured 3.3 ± 0.2 µm (3.1–3.5 µm) in length and 1.8 ± 0.1 µm (1.7–1.9 µm) in width. The polar tubules presented three to four turns. Phylogenetic analysis placed the new species within a clade containing myxobolid species from South American characiforms fish and appears as a close species of Myxobolus piraputangae and Myxobolus umidus. Nevertheless, the sequences of the new species and P. umidus and P. piraputangae have a large genetic divergence of 12 and 12.2% in their 18S rDNA gene, respectively. To the best of our knowledge, this is the first report of a Myxobolus species parasitizing the tetra fish mato-grosso, thus increasing our knowledge of cnidarian myxosporean diversity from South America.