Phytophthora infestans, the pathogen responsible for causing late blight in potato and tomato, is a rapidly evolving and highly adaptable pathogen. Following the appearance of a new clonal genotype in Kenya (KE-1 lineage) in 2007, there was a need to document possible displacement of the US-1 genotype by the newer lineage. Samples from Kenya (260) collected on potato and from Uganda collected on potato (134) and tomato (32) were genotyped with simple sequence repeat (SSR) and mitochondrial DNA haplotype (mtDNA) markers. Results show that, four years after its discovery, the KE-1 lineage has completely displaced the US-1 lineage on potato in Kenya. The KE-1 lineage has also migrated into Uganda through the eastern part of the country that borders western Kenya. All potato samples from eastern Uganda were of the KE-1 lineage. Moreover, samples from eight fields in western Uganda were also of the KE-1 lineage, which is in agreement with an ongoing westward displacement. However, the new lineage has not displaced the old lineage on tomato, as all samples from tomato were US-1. Principal coordinate analysis (PCA) scatter plots revealed clustering that indicated separation between the lineages and also between the subpopulations of the US-1 lineage on potato and tomato.