It is still unclear whether the masked palm civet (Paguma larvata) is native to the Japanese islands or introduced from the outside via human activities. In the present study, we sequenced the whole region (1,140 base-pairs) of the mitochondrial cytochrome b gene for 29 masked palm civets from Japan and Southeast Asia, and investigated their molecular phylogeography. Nine haplotypes were identified from the animals. Five halpotypes identified from 24 animals of Japan were clustered and separated from four haplotypes from five animals of Southeast Asia, showing clear differentiation between Japanese and Southeast Asian lineages. Sequence differences within Japanese haplotypes were smaller than those within Southeast Asian haplotypes and those between Japanese and Southeast Asian haplotypes. Within Japanese animals, all haplotypes found in eastern Honshu (Kanto district) were different from those of central Honshu (Chubu district). The present study highlighted the problem whether the Japanese Paguma larvata is an introduced species showing multiple original routes, or whether it is a native species genetically differentiated from Southeast Asian populations and even within Japan.