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Phytophthora infestans causes late blight of potato and tomato. In this study, two distinct groups of P. infestans isolates are reported based on morphological and molecular characters. The isolates were recovered from 300 single lesion leaf samples collected from potato in western and southern Ethiopia. The pathogen DNA was isolated from the single lesion dry leaves while live cultures were isolated from actively growing lesions of 100 leaves. Mitochondrial DNA (mtDNA) analysis clearly separated the isolates into two distinct groups. One of the groups corresponds to a known P. infestans mtDNA haplotype but the other is unique with a distinct Ic mtDNA haplotype and atypical morphological characters. DNA sequencing of the mtDNA confirmed that the isolates represented a previously unknown variant of P. infestans attacking Solanum tuberosum. In addition, the Ic mtDNA haplotype isolates produced papillate sporangia and chlamydospores that distinguished them from typical P. infestans isolates. All examined isolates were heterothalic and compatibility mating type A1. The novel group of the Ic mtDNA isolates constituted a single clonal population that had identical DNA fingerprint with a dominant lineage of the Ia mtDNA haplotype of P. infestans across nine microsatellite markers. This study provided new insight into a previously unknown variability within P. infestans in a region of the world where the pathogen population has rarely been studied. Further work is needed to understand the origins and significance of this finding.