A new species, Scutellaria austrotaiwanensis Hsieh & Huang from south Taiwan is described. This new species is similar to S. playfairi Kudo, but can be distinguished by its smaller leaves with 4 to 5 shallow crenations on the margins and the nutlet coat with short grappling-hook tuberculae. This new species differs from S. luzonica Rolfe by its rugulate-reticulate to reticulate and microperforate versus rugulate exinal ornamentation. This species is found on steep slopes between 400 and 500 m in Machilus dominated forest in south Taiwan. SEM micrographs of pollen grains and nutlets, and a chromosome number 2n=26 are provided.