"Magic mushrooms" (MMs) are psychoactive fungi containing the and Psychotropics Control Law in Japan. Because there are many kinds of MMs and they are often sold even as dry powders in local markets, it is very difficult to identify the original species of the MMs by morphological observation. Therefore, we investigated the rRNA gene for a large subunit (LSU) of several MMs to classify them by a genetic approach. In this paper, we described the phylogeny of species of MMs based on the partial sequence (about 970 bp) of the LSU and the rapid identification of MMs using the TaqMan PCR assay.