Limited knowledge is available on Phytophthora infestans populations in Sub-Saharan Africa (SSA). Therefore, and in response to recent severe late blight epidemics, P. infestans isolates from potato, tomato and Petunia × hybrida from eight SSA countries were characterized. Isolates were characterized with ‘old’ markers, including mating type (176 isolates), mitochondrial DNA haplotype (mtDNA) (281 isolates), glucose-6-phosphate isomerase (Gpi) (70 isolates), restriction fragment length polymorphism analysis with probe RG-57 (49 isolates), and by metalaxyl sensitivity (64 isolates). Most isolates belonged to the US-1 genotype or its variants (US-1.10 and US-1.11). The exceptions were genotype KE-1 isolates (A1 mating type, mtDNA haplotype Ia, Gpi 90/100 and unique RG-57 genotype), identified in two fields in Kenya, which are related to genotypes previously identified in Rwanda (RW-1 and RW-2), Ecuador and Europe. Metalaxyl-resistant P. infestans isolates from potato were present in all the countries except Malawi, whereas all the isolates from tomato were sensitive. Genotyping of 176 isolates with seven simple sequence repeat (SSR) markers, including locus D13 that was difficult to score, revealed 79 multilocus genotypes (MLGs) in SSA. When this locus was excluded, 35 MLGs were identified. Genetic differentiation estimates between regional populations from SAA were significant when locus D13 was either excluded (P = 0·05) or included (P = 0·007), but population differentiation was only low to moderate (FST = 0·044 and 0·053, respectively).