Japanese surnames have a complex origin. Some historical surnames derived from honorable titles given by the emperor of the time, while some surnames were brought by people from China or Korea. Afterwards, warriors dispersed through the war period and started using land names as their surnames. Therefore, the distribution of a surname reflects its origin and history. Even highly frequent surnames showed uneven geographical distribution, which can be explained by historical consequences. Surnames are also expected to work as a marker of clan members who share the similar genetic background. Since the 12th century, the surname of the family was inherited by sons, while daughters bore her husband’s surname after marriage. This paternal inheritance of the surname is similar with the genetic inheritance of Y chromosome. This article illustrates frequency maps of various surnames in Japanese prefectures based on telephone number book data, then compares the distribution of surnames with genetic backgrounds of the residents. Principle component analysis of surnames and genetic data showed similarity of the plot patterns when focued on local areas.