32 pomelos from domestic and international pomelo germplasms were used to study the genetic relationship between the green-skinned and red-fleshed pomelos from the distinctive germplasm of Hekou，Yunnan Province，China，the major pomelo varieties in southern China，and some pomelo varieties in Southeast Asia.13 pairs of SRAP primers and 11 pairs of AFLP primers were screened for the amplification of pomelo genome to analyze the genetic diversity and phylogenetic structure of the pomelos studied.The results showed that the SRAP and AFLP markers produced 125 and 91 polymorphic bands，with an average polymorphism of 96.40% and 95.73%，respectively.The results of cluster analysis with UPGMA showed that genetic distance between green-skinned and red-fleshed pomelos from Hekou Yao Autonomous County，Honghe Hani and Yi Autonomous Prefecture，Yunnan Province，China and the Shatian pomelo from Rong County，Guangxi Zhuang Autonomous Region，China was small，while the special germplasm with green-skinned and red-fleshed Yunqing No.1 and No.2 from Hekou were grouped with the green-skinned and red-fleshed pomelos from Vietnam，differing from the other 16 green-skinned pomelos.The genetic distance between No.513 and No.408 green-skinned pomelos from Hekou was small.No cases of synonymy or homonymy were found among the 18 green-skinned and red-fleshed pomelos studied.It is indicated that SRAP and AFLP markers can be effectively used for the study of genetic relationships between pomelos to clarify the genetic structure of population in the pomelos from domestic and international pomelo germplasms and the genetic background of pomelo varieties No.1 and No.2 with the local characteristics from Hekou.