A new Myxobolus species is described infecting gill filaments of the endangered ornamental fish Otocinclus cocama from Peruvian Amazon. In a total of 35 fish examined, five (14.3%) had myxozoan plasmodia. Taxonomic analysis was performed integrating multiple characters, including morphometrical, biological traits, ssrDNA sequence data and host ecological characters. Myxospores of M. iquitoensis n. sp. were ovoid in shape from the frontal view and measured 17.6±1.2 µm (16.2–19.8 µm) in length and 10.5±0.7 µm (9.8–12 µm) in width. The two polar capsules were elongate in shape, equal in size and occupying almost half of the myxospore body. They measured 8.7±0.4 µm (6.9–9.3 µm) in length and 3.3±0.2 µm (3–3.6 µm) in width. The polar tubules presented six to seven turns. Molecular phylogenetic analysis revealed that the obtained ssrDNA sequence did not match any existing sequences in GenBank but showed M. iquitoensis n. sp. to be a close species of M. figueirae. Nonetheless, the ssrDNA sequences of those species show large genetic divergence. This is the first description and phylogenetic study of a myxozoan parasitizing fish of the genus Otocinclus from South America, as well the first report of these parasites infecting a fish belonging to the Loricariidae family from Amazon basin. Considering the endangered status of the host, the high degree of host-specificity of freshwater histozoic myxobolids, the low occurrence shown by the new myxozoan, and the fact that this is the only host known for this myxozoan, the conservation status of the new species of myxozoan is likely to be connected to the future survival of its host.