Aspidistra Ker Gawl. is one of the the most diverse and fastest-growing genera of angiosperm. Most Aspidistra species have been discovered in a limited area or a single site through morphological comparison. Because of the lack of population studies, morphological variation within species and the boundaries of some species remain unclear. In recent years, combining genetic and morphological markers has become a powerful approach for species delimitation. In this study, we performed population sampling and integrated morphometrics and microsatellite genetic diversity analyses to determine the species diversity of Aspidistra in Taiwan. We identified three species, namely Aspidistra attenuata Hayata; A. daibuensis Hayata var. daibuensis; A. mushaensis Hayata var. mushaensis; and reduced A. longiconnectiva C.T.Lu, K.C.Chuang & J.C.Wang to the variety level, and described a new variety, A. daibuensis Hayata var. longkiauensis. The description, diagnosis, distribution, and photographs of this new variety as well as a key to the known Taiwanese Aspidistra are provided.