Black sigatoka (black leaf streak) caused by the fungus Mycosphaerella fijiensis, and yellow sigatoka caused by M. musicola, are common foliar pathogens of Musa species. Both species are pathogenic on East African Highland bananas (Musa spp. AAA) and may occur together on the same plant. A comprehensive diagnostic survey in Uganda in 1992 confirmed the presence of sigatoka leaf spots at most of the survey sites, but in most cases the species involved could not be determined due to the similarity of the symptoms they produce. In this follow-up survey in 1994, a polymerase chain reaction-based technique that differentiates the two pathogens was used to determine the distribution and incidence of the two pathogens on key banana genome groups grown in the country. The study revealed that M. musicola was present at all survey sites, and is more commonly found on exotic cultivars (banana clones not endemic to East Africa) than on the highland bananas. The cultivar Kayinja (ABB Pisang awak) had the highest incidence of M. musicola. Black sigatoka was not detected on plants grown at altitudes above 1350 m, but where it was found, it was present on all the cultivars at differing levels of severity. At and below an altitude of 1350 m the two pathogens were present on all cultivars but causing different levels of damage.