The Y Alu polymorphic (YAP) element and the Y-linked tetranucleotide repeat (GATA)_n of microsatellite locus DYS19 have been examined in Korean populations to raise the possibility of tracing paternal lineages and male-mediated gene flow between Korea and Japan. The frequency of YAP element was found to be 1% (3/301). This result is consistent with previous reports that showed the YAP element to be absent in most Asian populations and the high freqency of the YAP element in Japanese. The YAP chromosomes detected in this study appeared to be YAP haplotype 3, which is freqently found in the Japanese population. On the basis of the result for the locus DYS19 (n=252), Korean populations appear to have the most similar allelic frequency (C>D>B>E>A) to Mongolian populations among Asian populations. Although the DYS19 1ocus distinguishes the Japanese population (C>D>E>A>B) from most Asian populations, they tend to be somewhat closer to the result of the Korean population, with regard to the frequency of D allele. Finally, all of these results support the hybridization theory that modern Japanese populations have resulted from the ancient Jomon people (YAP^+) and Yayoi immigrants (YAP^-) from Korea.