The genetic structure of Puccinia graminis f.sp. tritici isolates sampled in three different regions of Ethiopia in 2006 and 2007 was investigated using 20 SSRs assuming sexual as well as asexual reproduction. Assays showed a high level of genetic diversity within P. graminis f.sp. tritici populations in Ethiopia in both modes of reproductions. Tests for population subdivision revealed the absence of genetic differentiation among the populations based on geographical separation as reflected by a low coefficient of genetic differentiation (≤0.046) and a single cluster consisting of all isolates. Gene flow among populations was estimated to be high (10 per generation). This study shows that the pathogen population of Ethiopia is characterized by a high genetic diversity within each population and absence of segregation among populations. Information obtained from this study may serve as a basis to develop better strategies for deployment of resistance genes, e.g. using marker-assisted combination of resistance alleles to achieve better control of wheat stem rust in Ethiopia.