This study describes a new microsporidian species from the adipose tissue of Diaphanosoma leuchtenbergianum collected from a eutrophic water body of Lianyungang city, Jiangsu province, China. Infected cladocerans exhibited opacity due to the accumulation of numerous spores in the adipose tissue. The earliest stages observed were uninucleate meronts which were in direct contact with the host cell cytoplasm. Multinucleate sporogonial plasmodia underwent plasmotomy to form uninucleate sporoblasts. Mature spores were ovoid, monokaryotic, and measured 4.80 ± 0.37 (4.09-5.23) µm in length and 2.64 ± 0.15 (2.34-3.01) µm in width. The polaroplast was bipartite with the tightly packed anterior lamellae and posterior tubules. The isofilar polar filament coiled in 9-10 turns and arranged in 2-3 rows. The exospore was covered with tubular projections and consisted of four layers. Phylogenetic analysis based on the SSU rDNA sequence indicated that the present species clustered with two Neoflabelliforma species (N. dubium from freshwater oligochaetes and N. aurantiae from freshwater daphnia) and an unidentified microsporidium from soil with high support values to form a solitary branch in microsporidia. Based on the morphological characteristics, ultrastructural features, and SSU rDNA-inferred phylogeny, a new species was named as Neoflabelliforma leuchtenbergianum n. sp.