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Although most Myxozoa species of the genera Ceratomyxa and Ellipsomyxa have been described in marine hosts worldwide, an increasing diversity has been reported infecting South American freshwater fish, mainly in Amazonian waters. The present study deals with two species of myxozoan ceratomyxids parasitizing the gallbladder of Amazonian ornamental cichlids fish: Ceratomyxa amazonensis is identified from a new host—Geophagus altifrons; while Ellipsomyxa santarenensis n. sp. is described infecting Satanoperca jurupari. Morphological (light microscopy and transmission electron microscopy), molecular (small ribosomal subunit DNA—SSU-rDNA sequencing) and phylogenetic analyses were used to characterize both species. Ceratomyxa amazonensis showed a prevalence of 64.2%, with plasmodia showing a vermiform shape and motility. For E. santarenensis n. sp., the prevalence was 33.3%. Ultrastructural analysis revealed that the vermiform C. amazonensis plasmodia were composed of an outer cytoplasmic region and a large vacuole occupying the inner area. In E. santarenensis n. sp., cytoplasmic expansions were observed in pseudoplasmodia originating pseudopodia. SSU rDNA sequencing-based genetic distance analysis revealed a very small difference between C. amazonensis, parasite of G. altifrons, and C. amazonensis, parasite of S. discus—host of the original description, thus showing that they are the same species occurring in a new host. For Ellipsomyxa santarenensis n. sp., molecular data revealed a difference of 1.6% for Ellipsomyxa amazonensis and Ellipsomyxa paraensis. The phylogenetic analysis revealed the grouping of E. santarenensis n. sp. together with the other freshwater Ellipsomyxa species of the Amazonian region, and associated with the morphological data, it was possible to identify it as a new taxon within the genus Ellipsomyxa. Full article