Quercus is considered as one of the most important genera in the Northern Hemisphere as its economic and ecological importance.Oaks are taxonomically perplexing due to interspecific shared morphological traits and intraspecific morphological variation,which mainly attributed to hybridization.Universal plastid markers could not provide sufficient variable sites to explore the phylogeny of this genus and chloroplast genome-scale data proved to be useful to resolve intractable phylogenetic relationships.