Vararia is a species-rich genus in the family Peniophoraceae and has been shown to be polyphyletic. In this study, sequences of ITS and LSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed with the maximum likelihood, maximum parsimony, and Bayesian inference methods. Seventeen lineages including six new species from China, i.e., V. fissurata, V. lincangensis, V. punctata, V. isabellina, V. sinensis, and V. yaoshanensis were recognized, in which V. fissurata is characterized by the brittle basidiomata with pruinose and cracking hymenophore having white to olivaceous buff hymenial surface, the clamped generative hyphae, presence of the two types gloeocystidia; V. lincangensis is characterized by the simple-septa generative hyphae, and thick-walled skeletal hyphae, and ellipsoid basidiospores; V. punctata is delimited by its thin to slightly thick-walled generative hyphae, and thick-walled skeletal hyphae, present thick-walled, clavate to cylindrical gloeocystidia; V. isabellina is characterized by having the cream to isabelline to slightly brown hymenial surface, thin to slightly thick-walled generative hyphae, and sub-fusiform to navicular basidiospores; V. sinensis is distinguishable by its white to slightly pink hymenial surface, thick-walled skeletal hyphae, and sub-fusiform to navicular basidiospores; V. yaoshanensis is characterized by cream to pinkish buff to cinnamon-buff hymenial surface, slightly thick-walled generative hyphae, the presence of two types gloeocystidia, and slightly thick-walled, ellipsoid basidiospores. Phylogram based on the ITS+nLSU rDNA gene regions included nine genera within the family Peniophoraceae as Amylostereum, Asterostroma, Baltazaria, Dichostereum, Michenera, Peniophora, Scytinostroma and Vararia, in which the six new wood-inhabiting fungi species were grouped into genus Vararia. The phylogenetic tree inferred from the combined ITS and LSU tree sequences highlighted that V. fissurata was found to be the sister to V. ellipsospora with strong supports. Additionally, V. lincangensis was clustered with V. fragilis. Furthermore, V. punctata was retrieved as a sister to V. ambigua. Moreover, V. sinensis was grouped with five taxa as V. breviphysa, V. pirispora, V. fusispora, V. abortiphysa and V. insolita. The new species V. isabellina formed a monophyletic lineage, in which it was then grouped closely with V. daweishanensis, and V. gracilispora. In addition, V. yaoshanensis was found to be the sister to V. gallica with strong supports. The present results increased the knowledge of Vararia species diversity and taxonomy of corticioid fungi in China. An identification key to 17 species of Vararia in China is provided.