We explored the genetic diversity and population genetic structure of an invasive alien species, the raccoon Procyon lotor, which was introduced into the Shikoku Island of Japan, using sequences of the mitochondrial control region and 10 polymorphic microsatellite loci. In 80 individuals examined, we detected two genetically divergent haplotypes, indicating that two maternal lineages had been introduced into Shikoku Island. Population clustering analysis suggested the nonexistence of genetic structure in the area. The relatedness network showed that the raccoon population in Shikoku Island consisted of closely related individuals. The genetic diversity of the Shikoku raccoon population was lower than that in the native range. These results and a prior report indicate that the Shikoku raccoon population is likely to have expanded from small numbers of founders originating from an initial invasive population. Raccoon captures outside Kagawa are decreasing, although past expansions into Tokushima and Ehime suggest that there are no geographical barriers among these areas. Therefore, action should be taken to prevent any re-expansion of the raccoon population in Kagawa. Intensive monitoring and the elimination of dispersers from Kagawa, as well as effort to eradicate potential source populations for expansion in Kagawa, are needed.