Inter-simple sequence repeat(ISSR) were used to detect the genetic diversity among 38 bottle gourd accessions from 7 provinces in China.Twelve ISSR primers produced 96 polymorphic bands,with averaged 8 polymorphic bands each primer pair.The average percentage of polymorphic bands was 83.5%.38 accessions were clustered into 4 groups and 8 subgroups based on the ISSR data by the method of clustering analysis,and 4 groups and 10 subgroups by the method of principal coordinates analysis.The results from ISSR molecular markers showed obvious correlation with the agronomic characteristics classification and the geographical distribution of the bottle gourd accessions.