Kratom is the leaves of Mitragyna speciosa (Rubiaceae). Recently, kratom has been sold in street shops or on the Internet in Japan for the purpose of abuse due to its opium-like effects. In this study, we investigated the botanical origin of the commercial kratom products using the internal transcribed spacer (ITS) sequence analysis of rDNA in preparation for future regulation of this product. In addition, a previously reported method to authenticate the plant, utilizing polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was applied to the same products in order to estimate the method's accuracy and utility. The ITS sequence analysis of the commercial kratoms revealed that most of them were derived from M. speciosa or closely related plants, while the others were made from the same tribe plant as M. speciosa. The reported PCR-RFLP method could clearly distinguish kratoms from the other psychoactive plants available in the Japanese markets and also from related plants. The authentication method is considered to be useful for the practical regulation of the plant due to its wide range of application, high accuracy and simplicity.