Rapid flagement length polymorphism (RFLP) and amplified flagement length polymorphism (AFLP) analyses were used to study genetic diversity of Cercospora zeae-maydis
isolates collected from Uganda, Kenya and Rwanda. For comparative purposes, isolates from Zimbabwe and the United States of America (USA) were included. Phylogenetic analysis of AFLP data revealed two major clusters. One large cluster comprised of 75 African and US group II isolates and the second comprised cluster of 4 USA group I isolates. Similar groupings were observed with RFLP data. Analysis of molecular variation (AMOVA) based on AFLP data revealed a significant population structure between American and African populations (ϕ FST
= 0.07). No population structure was detected, among African isolates (ϕFST
= 0.01), while a strong and significant structure was obtained between the two pathotypes (ϕ FST
= 0.19). The AMOVA using RFLP data, showed absence of a population structure among African populations (ϕ FST
= 0.01), and gene flow among African populations was high (49.5). These findings suggest that group II pathotype is predominant in East Africa and gene flow appears to be the fundamental evolutionary force accounting for the current genetic structure. A regional approach to abate epidemics is most suitable.