The neogregarine Apicystis bombi is considered a low prevalence parasite of Bombus spp. Before our work it has only once been detected in one single specimen of the Western honeybee Apis mellifera. This contribution reports the presence of A. bombi parasitizing both A. mellifera and Bombus terrestris at a site in Northwestern Argentine Patagonia (Bariloche, close to the border with Chile) and analyses its possible absence in the Pampas region, the most important beekeeping region of the country. In Bariloche, prevalence of A. bombi in A. mellifera was 7.6% in 2009, and 13.6% in 2010, whereas in B. terrestris it was 12.1%. Infections were not detected in 302 bee hives periodically prospected along 3 years (almost 400 000 honeybee specimens) in the Pampas. Analysis with the probability program FreeCalc2 suggested a possible absence of A. bombi in this area. Because of high virulence showed in several species of Bombus in the Northern hemisphere, A. bombi should be closely monitored in A. mellifera and in native Bombus species or other Apidae.