A severe outbreak of late blight on potato occurred in central Taiwan in the winter of 1997. Subsequently, the disease spread to potato and tomato fields over the entire island within 2 months. Since that time, late blight has become endemic and poses a significant threat to potato and tomato production throughout Taiwan. To understand why the causal agent Phytophthora infestans has caused such severe epidemics of late blight in Taiwan, diseased plant samples were collected from the major potato- and tomato-growing areas of Taiwan from the 1997 outbreak to 2002, and compared with isolates collected prior to the 1997 outbreak. Among the 11 isolates collected prior to the 1997 outbreak, all were of the US-1 lineage, with the following characteristics: A1 mating type, metalaxyl sensitivity, Gpi genotype of 86/100, Pep genotype of 92/100 or 100/100, mtDNA haplotype of Ib, and DNA fingerprint pattern of US-1 (n = 7), US-1.2 (n = 1), or US-1.3 (n = 3). In contrast, 83 isolates collected from the 1997 outbreak through 2002 displayed moderate to high levels of metalaxyl insensitivity, Gpi genotype of 100/100/111, Pep genotype of 100/100, mtDNA haplotype of IIb, and DNA fingerprint pattern of US-11 or its variants. These results suggested that, during 1997–1998, the US-1 population of P. infestans was rapidly displaced by the US-11 clonal lineage, possibly introduced into Taiwan with latently infected potato tubers from overseas.