It was studied that the genetic diversities and phylogenetic relationships of 48 Bougainvillea germplasm based on RAPD and ISSR markers in this paper.The results were as follows:(1)The polymorphism was identified by 7 RAPD primers and 11 ISSR primers in the germplasm.97 bands were amplified by RAPD,and 140 bands by ISSR,the polymorphic rate of both markers was 100％.(2)The cluster analysis (UPGMA) showed a higher genetic diversity level based on those polymorphic bands amplified with ISSR and RAPD primers.The genetic similarity coefficient ranged from 0.318 8 to 0.955 6 by RAPD,and from 0.349 5 to 0.900 0 by ISSR.(3)48 samples can be clearly distinguished,and their clustering groups were basically consistent by two markers except a little difference between them.These samples generally originated from two germ lines,of one was from B.glabra,and mainly intraspecific origin,while the other was from species including B.spectabilis,B.peruviana,B.×buttiana and B.×spectoglabra,so the germplasms component were more diverse.(4)The genetic similarity of two markers had a significant correlation (r=0.752 3).The resolution of the molecular markers RAPD and ISSR is more reliable than morpho-agronomic characters to identify individual cultivars according to this investigation.