We provide the first evidence for inter-specific warfare in bees, a spectacular natural phenomenon that involves a series of aerial battles and leads to thousands of fatalities from both attacking and defending colonies. Through molecular analyses of fights at a study hive of the Australian stingless bee, Tetragonula carbonaria, we revealed an attack launched by a related species, T. hockingsi, which has only recently extended its habitat into southeastern Queensland. Following a succession of attacks by the same T. hockingsi colony over a four-month period, the defending T. carbonaria colony was defeated and the hive usurped, with the winning colony installing a new queen. We complemented our direct observations with a longitudinal study of over 260 hives over five years, and found interspecies hive changes, which were likely to be usurpation events, occurring in 46 Tetragonula hives over this period. We discuss how fighting swarms and hive usurpation fit with theoretical predictions on the evolution of fatal fighting, and highlight the many unexplained features of these battles that warrant further study.