Bees are key species for pollination and apiculture. Within the multiple biotic threats, parasites are one of the main players involved in bee health. Among them, trypanosomatid parasites have been the focus of recent studies that have placed them as one of the most prevalent microorganisms in the digestive tract of bees around the world. Here, we review what is known in epidemiology, cell biology and genetics of these parasites in bees with a particular focus on the work made on honeybees. We also discuss the possible implications for honeybee health and describe research gaps to be explored both from the honeybee host and trypanosomatid parasites sides.