Species of the genus Ellipsomyxa Køie, 2003, parasitize mostly marine and brackish fish around the world. In the present study, we describe two novel species of Ellipsomyxa: Ellipsomyxa plagioscioni n. sp. parasitizing the gall bladder of Plagioscion squamosissimus (Sciaenidae), a freshwater fish but commonly found in brackish water in the Amazonian estuarine environment; and Ellipsomyxa paraensis n. sp. infecting Cichla monoculus (Cichlidae), a strictly freshwater fish. The host specimens were caught from the Amazon and Tapajós rivers, in the municipal region of Santarém, in the State of Pará, Brazil. The study was performed using a combination of morphological, biological, and SSU rDNA-based phylogeny, which suggested that marine transgressions of the Miocene epoch, in the central region of South America, were a pathway for the adaptation and radiation of these cnidarian parasites in the freshwater environment. Both disporic plasmodia and mature myxospores were found floating freely in the bile. Mature myxospores from both species were ellipsoidal in the valvular and sutural views, with thin smooth valves elongated in the direction perpendicular to the plane of the transverse sutural line. Ellipsomyxa plagioscioni n. sp. myxospores measured 11.1 (10.2–12.8) µm in length and 6.6 (5.6–7.6) µm in width. Two pyriform polar capsules discharging on opposite sides, some distance from both the sutural line and the spore ends, measured 3.8 (3.2–4.4) µm in length and 2.8 (2.3–3.3) µm in width, with 5–6 coil polar tubules. Ellipsomyxa paraensis n. sp. myxospores measured 11.5 (10.5–12.4) µm in length and 7.5 (6.6–8.6) µm in width. Two pyriform polar capsules which discharged on opposite sides some distance from both the sutural line and spore ends, measured 3.2 (2.1–3.9) µm in length and 2.6 (2.0–3.3) µm in width, with 2–3 coil polar tubules. Valvular protrusions were observed, associated with the tips of the polar capsules. Molecular analysis based on the SSU rDNA sequences indicated that the two novel Ellipsomyxa species were distinct from all other sequences deposited in the GenBank database. The phylogenetic trees clustered E. plagioscioni n. sp. as a basal species of a lineage of the marine/estuarine Ellipsomyxa, while E. paraensis n. sp. clustered together with other Amazonian species.