Myxobolus ampullicapsulatus n. sp. was isolated from the gills of Carassius auratus auratus (L., 1758) in Chongqing, China. Myxospores were pyriform, measuring 16.5–19.5 μm long × 8.5–10.0 μm wide × 7.0 μm thick. Two equal polar capsules were ampullaceous, measuring 7.0–10.0 μm long × 2.5–4.0 μm wide, containing polar filaments coiled 9–10 turns. Spore length of this species exceeds that of the majority of other Myxobolus spp., and those overlapping in this dimension can be differentially diagnosed by other characters. Furthermore, the small subunit ribosomal DNA (SSU rDNA) of M. ampullicapsulatus n. sp. is unique among myxozoans sequenced to date. Phylogenetic analyses of the SSU rDNA gene sequence placed this species in a clade composed exclusively of gill parasites, most closely related to Myxobolus longisporus, which also infects the gills of cyprinid fishes in China.