Avian schistosomes, mainly belonging to the genus Trichobilharzia, are the etiological agents of cercarial dermatitis in humans. The aims of this study were to report a human case of cercarial dermatitis contracted in a paddy field in a natural regeneration area in Tokyo, Japan, and identify the etiological agents of this case using molecular phylogenetic analyses. A snail survey was conducted between 2021 and 2023 in a rice paddy field where a case of cercarial dermatitis occurred, and molecular phylogenetic analyses of the furcocercariae and parasitized lymnaeid snails were performed based on the partial sequence of the mtDNA cox1 gene. Furcocercariae were detected in 11 (2.7%) of the 413 lymnaeid snails examined, and all 120 pleurocerid snails tested negative for cercariae. The cercarial larvae possessed a pair of eye spots and a characteristic bifurcated tail. Phylogenetic analyses of the cox1 genes identified the furcocercariae as Trichobilharzia sp., and the lymnaeid snails were Radix plicatula. This study demonstrated that the life cycle of a Trichobilharzia sp., using R. plicatula as an intermediate host, is established in an urban natural restoration area in Tokyo, serving as a source of human cercarial dermatitis. This study emphasizes the need for an increased awareness of cercarial dermatitis as a potential public health concern.