Rubus is a large and taxonomically complex genus consisting of hybrid and polyploid.In this review,we summarized and discussed the application of DNA sequences in the Rubus L.phylogenetic studies,mainly focus on their limitation and promising application prospect in the Chinese Rubus.Noncoding chloroplast DNA fragments combined with ITS sequence were frequently applied.ITS was the most widely applied sequence among the nDNAs.It has been used for clarifying the phylogeny between sections Idaeobatus and Malachobatus,illustrating genetic relationship among Rubus cultivars,and identifying the origin of hybrid and polyploid.Due to ITS polymorphism among individuals,it was necessary to detect putative pseudogenes.By contrast,low-copy nuclear genes were rarely applied except GBSSI and LEAFY.The phylogenetic relationships of some Rubus species remain unclear because of the deficiency of available DNA sequence and limitation of covered groups.Additionally,utilization of multi-specific DNA and more samples in phylogenetic applications probably has one bright future,along with the morphology,palynology,cytology and other means.