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The new microsporidium, Agglomerata connexa sp. nov., is described, based primarily on ultrastructural characteristics. The parasite infects the adipose tissue of Daphnia longispina O.F. Müller, 1785. All life cycle stages have isolated nuclei. Sporogonial reproduction is by rosette- or finger-like budding. Sporophorous vesicles contain not more than 4 mature spores, most vesicles are monosporous, and usually devoid of inclusions. Rare aggregates of tubules are visible inside multisporous and outside of individual sporophorous vesicles. Often two or more individual vesicles form a chain-like structure. Unfixed spores are pyriform, measuring 4.08 ± 0.27 x 2.72 ± 0.24 mm. The exospore is layered, approximately 30 nm thick. The polar filament is isofilar, 140 nm wide, making 5-7 coils in the posterior half of the spore. The polaroplast has three subdivisions: wide lamellae, narrow lamellae and tubules. Discrimination from other microsporidean species is discussed.