The genus Myricaria belongs to the family Tamaricaceae, which consists of thirteen species, ten of which are distributed in China. They are riparian or lake-side shrubs and naturally occur in eastern Asia, extending to central Asia and Europe, with a suggested center of origin and diversity in the Himalayan region. Most of the species are threatened by increasing habitat fragmentation and anthropogenic disturbances like dam and highway construction and over-grazing. Information oil molecular phylogenetic relationships is critical for understanding the taxonomy and developing conservation strategies for Myricaria species in China. In the present Study, DNA sequence data from the nuclear ribosomal internal transcribed spacer region and the plastid psbA-trnH intergenic spacer were used to infer the phylogeny of the genus. Thirteen morphological traits were also used in conjunction with the molecular phylogenetic relationships. The phylogenetic analysis revealed a basal clade of M elegans to other Myricaria species. Molecular evidence resolved one suspicious specimen Myricaria sp. that was closely related to M. wardii. Furthermore, the results revealed that three widespread species-M. paniculata, M bracteata and M squamosa-with little morphological difference have distinct DNA sequences. On the other hand, M pulcherrima and M. platyphylla were found to be grouped with the above three widespread species despite their morphological characters being similar to that of M elegans. Also, M laxiflora was found in a more basal phylogenetic position than M paniculata although the two species are morphologically similar. Our phylogenetic analyses provided Molecular evidence in Supporting the hypothesis that the center of origin and evolution for Myricaria species is the Himalayan region. The present study provides useful baseline data for formulating conservation priorities and further taxonomic delineation.