Nosema apis is a microsporidian that invades the intestinal tracts of adult bees and causes nosema disease, also known as nosemosis. Nosema is also associated with Black queen-cell virus. Nosema is normally only a problem when the bees can not leave the hive to eliminate waste (for example, during an extended cold spell in winter or when the hives are enclosed in a wintering barn). When the bees are unable to void (cleansing flights), they can develop dysentery.

Nosema is treated by increasing the ventilation through the hive. Some beekeepers will treat a hive with antibiotics.

Nosema can also be prevented or minimized by removing much of the honey from the beehive then feeding the bees on sugar water in the late fall. Sugar water made from refined sugar has lower ash content than flower nectar, reducing the risk of dysentery, and may have essentially the same nutritional content, although this remains a point of controversy among some beekeepers.

In 1996, a similar type of organism to Nosema apis was discovered on the Asian honey bee Apis cerana and subsequently named Nosema ceranae. This parasite apparently also infects the Western honey bee.

It has been reported that exposure to corn pollen containing genes for Bacillus thuringiensis (Bt) production may weaken the bees' defense against Nosema. In this study, it is stated that in relation to feeding a group of bees with Bt corn pollen and a control group with non-Bt corn pollen, that: "in the first year the bee colonies happened to be infested with parasites (microsporidia). This infestation led to a reduction in the number of bees and subsequently to reduced broods in the Bt-fed colonies as well as in the colonies fed on Bt-toxin-free pollen. The trial was therefore discontinued at an early stage. This effect was significantly more marked in the Bt-fed colonies. (The significant differences indicate an interaction of toxin and pathogen on the epithelial cells of the honeybee intestine. The underlying mechanism which causes this effect is unknown.)" This study should be interpreted with caution given that there was no repetition of the experiment nor any attempt to find confounding factors. In addition, it is noteworthy that BT toxin and transgenic BT pollen showed no acute toxicity to any of the life stages of the bees examined, even when the BT toxin was fed at concentrations 100 times that found in transgenic BT pollen from maize.