Five new species of the genus Daphnephila (Diptera: Cecidomyiidae: Asphondyliini), D. ornithocephala, D. stenocalia, D. sueyenae, D. taiwanensis, and D. truncicola, all associated with Machilus thunbergii (Lauraceae), are described from Taiwan, and one previously known species, D. machilicola, is redescribed from Japan. Among the five new species, D. truncicola induces stem galls and the other four species induce leaf galls. A molecular phylogenetic analysis based on partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene suggests that in this genus the stem-galling habit is a more ancestral state compared to the leaf-galling habit. Daphnephila seems to be of tropical origin and to have dispersed to Japan through Taiwan.