The smooth cordgrass, Spartina alterniflora Loisel, is an aggressive invasive species that significantly impacts coastal ecosystems worldwide. Native to the eastern United States, it has rapidly spread along East Asian coasts and was unintentionally introduced into Korea, leading to the devastation of native ecosystems. This study examines the population genetic structure and invasion pathway of S. alterniflora along Korean coasts using chloroplast DNA (cpDNA) fragments and nuclear ITS. Our results revealed that the S. alterniflora population in Korea primarily consists of two geographically isolated haplotypes (C1 and C4). Furthermore, two individuals were found to have haplotype N, potentially a newly discovered haplotype in this study. The haplotypes C1 and C4 are widely distributed in the both the native population and the introduced population in East Asia. Thus, the presence of these two haplotypes in different localities in Korea suggests multiple invasion events. The phylogenetic tree from the nuclear ITS showed no significant genetic variation between regions. Comparisons of the cpDNA data of this study with the available GenBank data from the native range in the U.S. and the invasive range in East Asia (China and Japan) revealed that the East Asian population (China, Japan, and Korea) is nearly homogeneous (AMOVA; Fst = 0.06871, p = 0.5). Our findings suggest that the C1 and C4 haplotypes might have been introduced into Korea at least two times, possibly via natural dispersal and/or transport vectors. This emphasizes the importance of strengthening coastal management to prevent further spread.