A new species of Myxosporea, Henneguya nagelii n. sp., is described parasitizing the gills of Cyphocharax nagelii collected from Peixe's River, São Paulo State, Brazil. Among the fish examined, 16.7% had gills parasitized by myxosporeans. The plasmodia were white, round, or oval and measured 150-250 μm. The mature spores were fusiform and had smooth wall. The spores measurements were the following: total length, 34.5 ± 4.2 (26.4-39.9) μm; body length, 12.0 ± 0.5 (11.2-11.9) μm; body width, 4.9 ± 0.3 (4.4-5.5) μm; and caudal process length, 22.4 ± 4.0 (14.7-27.3) μm. The polar capsules were elongated and of unequal size, with lengths of 4.9 ± 0.4 (4.0-5.9) μm and 5.2 ± 0.4 (4.6-6.0) μm for the longest and shortest axes, respectively. Capsule width was 1.8 ± 0.2 (1.5-2.2) μm. Each capsule contained a polar filament with six to eight turns. There was no mucous envelope or iodinophilous vacuole. Morphometric differences between this parasite and other species of the genus Henneguya indicated that the parasite observed in C. nagelii is a new species. This is the first species of Myxosporea described in Peixe's River.