The microsporidium Nosema neumanni n. sp., a new parasite of the honeybee Apis mellifera is described based on its ultra-structural and molecular characteristics. Structures resembling microsporidian spores were found by microscopic examination of honeybees from Uganda. Molecular confirmation failed when PCR primers specific for Nosema apis and Nosema ceranae were used, but was successful with primers covering the whole family of Nosematidae. We performed transmission electron microscopy and found typical microsporidian spores which were smaller (length: 2.36 ± 0.14 μm and width: 1.78 ± 0.06 μm; n = 6) and had fewer polar filament coils (10–12) when compared to those of known species infecting honeybees. The entire 16S SSU rRNA region was amplified, cloned and sequenced and was found to be unique with the highest resemblance (97% identity) to N. apis. The incidence of N. neumanni n. sp. in Ugandan honeybees was found to be much higher than of the two other Nosema species.