ISSR (inter-simple sequence repeat) molecular markers were employed to investigate the genetic relationship among 33 species of Begonia.We chose 13 polymorphic primers from 70 primers to analyze their genetic relationships with popgen32 software.UPGMA results showed that the genetic distances among the 33 Begonia species were between 0.188 9 and 0.932 8,the polymorphism percentage is 97.54% and the Shannon diversity index was 0.551 9,the Nei’s gene diversity index was 0.376 0.With their rich genetic variations,the UPGMA analysis goes well with the recent classifications.With similar ecological and geographical conditions,the populations clusters firstly.