A new microsporidian species was described from the freshwater shrimp Caridina gracilipes collected from Lake Luoma located in Northern Jiangsu province, East China. The infected shrimps appeared generally opaque due to the presence of white cysts located in the connective tissues of the surface of the hepatopancreas. The earliest developmental stages observed were diplokaryotic meronts which were in direct contact with the host cell cytoplasm. Multinucleate sporogonial plasmodia developed into uninucleate sporoblasts which were enclosed in sporophorous vesicles. The parasite developed synchronously within an individual sporophorous vesicle. Mature spores were pyriform and monokaryotic, measuring 5.45 ± 0.18 (5.12–5.82) µm long and 3.57 ± 0.17 (3.18–3.92) µm wide. Anisofilar polar filaments coiled 10–12 turns and arranged in one row. Phylogenetic analysis based on the obtained SSU rDNA sequence indicated that the present species clustered with Triwangia caridina with high support value to form an independent branch which was placed at the basal position of a large clade of containing microsporidia of fishes, crustaceans and amphipods. Based on the morphological characters and ultrastructural features, as well as SSU rDNA-inferred phylogenetic relationships, a new species was erected and named as Triwangia gracilipes n. sp. The taxonomic affiliation of Triwangia was also primarily explored.