A new cnidarian myxosporean infecting the spleen of an economic and ecological important bryconid fish (Salminus franciscanus) is described based on integrative taxonomic approach including morphological, ultrastructural, biological traits, geography, molecular data and phylogenetic analysis. In a total of thirty specimens examined, nineteen (63.3%) were infected by an undescribed parasite species belonging to the genus Myxobolus. Plasmodial development was asynchronous, with young development in the periphery and mature myxospores in the central area and without projections and microvilli in the plasmodial wall. Mature myxospores were ovoid in shape and measured 7.9 ± 0.2 μm (7.6–8.1 μm) in length and 5.4 ± 0.1 μm (5.0–5.6 μm) in width. The two polar capsules were equal in size, occupying a little more than half of the myxospore body, measuring 4.0 ± 0.2 μm (3.9–4.1 μm) in length and 1.7 ± 0.1 μm (1.5–1.8 μm) in width. The polar tubules coiled in six turns, perpendicular to the long axis of polar capsule. Phylogenetic analysis placed the new species within a clade containing nine myxobolid species from South American characiforms fish and appears as a close species of Myxobolus pantanalis. Nevertheless, the sequences of the new species and M. pantanalis have a large genetic divergence of 13.5% in their SSU rDNA. In light of the differences observed from the integrative taxonomy, we confidently considered that this isolate is a new species of cnidarian myxosporean, M. douradae n. sp., increasing the knowledge of diversity of this enigmatic group of cnidarians.