Despite the increasing demand for diverse Centella asiatica (L.) Urb. species in Korea, studies on related topics are limited, with the majority of studies focusing on functional evaluations, rather than genetic diversity. Therefore, in this study, we explored the genetic diversity of C. asiatica, a valuable medicinal plant collected from six island regions in Korea, using genotyping-by-sequencing analysis. Specifically, we aimed to understand plant genetic variations, population structure and the potential for conservation and genetic improvement. The results indicated relatively high genetic diversity among the samples collected from the six island regions but low genetic differentiation among their populations. Two distinct genetic clusters were identified; however, even within these clusters, genetic differentiation was minimal. The lack of significant isolation-by-distance patterns and evidence of potential clonal spread suggested that some individuals that adapted to colder Korean conditions achieved dominance. This study highlights the importance of assessing the genetic diversity of native C. asiatica in Korea and explores the possibility of conducting follow-up studies to understand the phytochemical content and bioactivity variations among the individuals. This information can aid in the selection of superior resources and effective utilization of plant genetic resources for cultivar development and other applications.