In this study, we used three chloroplast DNA barcoding, ndhF, psbA-trnH and rps16, for cluster analysis of 98 bamboo species belonging to 17 genera collected from Fujian Province plant garden and then performed the analysis on the 43 known salt tolerant bamboo species. The results showed that the used three DNA barcodes had good generality for bamboos with average generality of above 96%. The psbA-trnH could not cluster the species and genera of Bambusoideae other than Guadua, but could cluster some salt tolerant bamboo species. The ndhF and rps16 barcode sequences could cluster some species and genera, and the clustering effect of salt tolerant bamboos in Dendrocalamus, Bambusa and Pleioblastus was better.