Uganda is the second largest producer of dry beans (Phaseolus vulgaris L.) in Africa, but common bean rust caused by Uromyces appendiculatus (Pers. Unger), is negatively impacting the production of the crop. There is little information on the occurrence and identity of the rust pathotypes present in the country. Consequently, a field survey was carried out during the 2015 second planting season in fifteen districts, representing the areas of high beans production in Uganda. High common bean rust incidence and severity were observed in the low altitudes and the South-Western Highlands of Uganda. Wakiso and Hoima districts had the highest rust disease incidence 72 and 76% respectively and severity rates of 6 and 5.5, respectively. Rust disease incidence was uniformly high on commercial genotypes and landraces. Similarly, high rust disease incidence and severity were observed in the bean-maize– groundnut cropping system. Twenty-three single rust isolates were collected in Uganda and inoculated on 11 bean rust differentials and Ouro Negro (Ur-14) genotypes. Six rust pathotypes were identified and these included 2-0, 4-0, 50-0, 5-1, 4-33 and 63-19. Five of the pathotypes were of Andean origin and only pathotype 4-33 was of Mesoamerican origin. The rust pathotype 63-19 showed similar pathogenic characteristics with the Puerto Rico rust race 19-63. This study provides critical baseline information to integrate breeding and crop protection in the efforts to develop an overall strategy for the management of common beans in Uganda.