333 samples of native poplars among 11 species collected from Southwest China were examined by SRAP (Sequence-related amplified polymorphism) markers to determine the genetic variation. The results showed that 7 selected primer combinations of SRAP generated 215 bands, of which, 158 bands were polymorphic. The percentage of polymorphic bands was 73.49%. All these index indicated that there were considerable genetic variation existed among 11 native poplar species. The variance components among species was 10.84 and it accounted for 48.70% of the total genetic variation by molecular variance analysis (AMOVA) indicating the genetic difference among 11 native poplar species was significant (P<0.001). The genetic similarity coefficients among the tested poplars ranged from 0.8199 to 0.9607, with an average of 0.8983. The cluster analysis showed that there was the smallest genetic difference between Populus qamdoensis and P. szechuanica var. tibetica, whereas the largest genetic difference between P. lasiocarpa and P. trinervis. The results of this research would provide a scientific basis for conservation, development and utilization of the native poplar gene resources in Southwest China.