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Myxosporeans are a diverse group of microscopic cnidarians of wide distribution that evolved into a parasitic lifestyle. A new myxosporean species, Myxobolus sp., is herein described infecting the mandible of wild specimens of Synbranchus marmoratus , caught in the world's largest tropical wetland area, Pantanal, Brazil. Light, scanning, transmission electron microscopy and histological observations unveiled detailed taxonomic information of the new myxosporean cnidarian. Ultrastructural analysis revealed a detailed description of plasmodia structures which can be used for comparison with plasmodia from other species of myxobolids. Both histological and ultrastructural observations evidenced a connective tissue capsule surrounding the plasmodia of Myxobolus sp. as a histopathological host reaction to the infection of this parasitic cnidarian. Histology showed that tissue tropism of the new myxosporean occurs in a well-defined part of the mandible, with development of plasmodia occurring in the epidermis layer. Mature myxospores from the valvular view featured an ovoid shape and had a short prolongation of the spore valves in the posterior end. Myxospores measured 22.7 ± 1.2 µm (21.5–23.9 µm) in length, 12.5 ± 0.4 µm (12.1–12.9 µm) in width and 11.3 ± 0.5 (10.8–11.8 µm) in thickness. Polar capsules were pyriform equally-sized and measuring 4.6 ± 0.3 µm (3.9–4.3 µm) in length and 2.9 ± 0.1 µm in width (2.8–3.0 µm). Finally, this study substantiates the still hidden myxosporean diversity from South America. • First report describing infection of Symbranchus marmoratus with myxosporean cnidarian from South America. • A new myxosporean cnidarian is described using detailed features obtained from light, scanning and transmission electron micrcoscopy. • This study provides detailed descriptive ultrastructural features which could suit as a basis for accurate taxonomic identification of this new myxoxporean cnidarian. • Ultrastructural features have been described in detail for plasmodia of the new myxosporean species. [ABSTRACT FROM AUTHOR]