The lichen mycota of the Imperial Palace Grounds, Tokyo, Japan was revised in the light of ITS rDNA sequences and updated knowledge. The following, formerly unidentified or misidentified species were revealed: Candelaria asiatica (as ‘C. concolor’) and Flavoplaca flavocitrina (as ‘Caloplaca aff. citrina’) are new to Japan, and Cladonia rei (as ‘C. ramulosa’), Pertusaria flavicans, Phaeographis pruinosa, and Phaeophyscia limbata (as ‘P. hispidula’) are new to the Imperial Palace Grounds. The ITS rDNA sequences for 31 species were successfully obtained from 81 specimens as well as 12 specimens collected from other places outside of the Imperial Palace Grounds. The BLAST search with registered sequences in GenBank was performed for each sample.