We studied the population structure of South Korea by using the distributions of surnames for all 246 administrative regions. Every 4,177 surnames are distinguished by their bon-gwan which indicates the place of their family clans. Using Fisher’s Alpha, we found that the level of inbreeding increases as the distance from the capital Seoul increases. We introduced the Shannon index to measure the level of spatial diffusion for each surname population, and the geographical clusters based on similarities of the surname compositions among the regions show almost exact agreement with those at the administrative districts.