Late blight disease caused by an Oomycete Phytophthora infestans is a major constraint to potato production and is causing significant yield losses in Ethiopia. This study was conducted to characterize the genetic diversity of the pathogen population in the major potato growing regions Awi, East Hararghe, South Gondar, West Arsi, West Gojjam and West Shewa in Ethiopia. In total 138 P. infestans isolates were collected using FTA cards in 2017, genotyped using 12-plex SSR markers and characterized for the mitochondrial haplotype. The genotypic patterns were compared to those of reference isolates from the EU2_A1 and US-1 clonal lineages. The population structure analysis using discriminant analysis of principal components (DAPC) and STRUCTURE indicated that most of the Ethiopian isolates were similar to the EU2_A1, while a second cluster of isolates was formed that was clearly different from EU2_A1 as well as the US-1 reference isolates. This new genotype was characterized by private alleles in the SSR D13 locus. We named this new genotype as ET-1 lineage. All isolates had the same mitochondrial haplotype (Ia). EU2_A1 was dominant clonal lineage in all locations except West Arsi which was dominated with ET-1 lineage. The old US-1 lineage was not discovered among the Ethiopian samples which suggest that it has been displaced. The West Arsi, West Gojjam and West Shewa populations were found to contain the highest genetic diversity, with the greatest number of multi locus genotypes (MLGs) and a higher diversity index compared to the other locations. The findings of this study establish a baseline of the pathogen population diversity in Ethiopia. Continuous tracking of P. infestans population in both potato and tomato is recommended to monitor the changes and migration patterns.