Mutations occur in Y chromosome genes similar to autosomal genes. However, unlike autosomal genes, Y chromosome genes do not undergo recombination, which produce distinctive characteristics and distribution patterns in different geographic regions. Therefore, detailed analysis of mutations of Y chromosome genes might provide information for personal identification or analysis of phylogenetic history. In Y-STR (short tandem repeat) analysis tests on 668 habitants of Jeju Island, the largest island in the Korean peninsula located apart from the mainland, a deletion at DYS448 was found in 10 samples. The length of deletion was estimated by confirming specific Sequence Tagged Site (STS) markers ranging from G66018 to sY1201. Patterns found were similar to those of the Kalmyks, a tribe that has had strong social and genetic influences in Jeju Island in the past. Historically from 1273 on, Jeju Island was governed by Mongolian for about one hundred years. The results of this study suggest such historical aspects affected the genetic composition of people living in Jeju Island. Furthermore, previous reports showed that Y chromosomal deletions and region specific Y chromosomal mutations depended on regional differences. This study may be useful for a better understanding of the genetic structure of Jeju habitants as well as Korean population for the purpose of forensic practice and population genetics.