Abstract: The genetic relationships between 22 flue-cured tobacco varieties were assessed by RAPD and ISSR markers.For RAPD analysis,13 random primers were identified with polymorphism among the entries.In total 167 bands were produced,of which 50 bands were polymorphic.Percentage of polymorphic bands was 29.9%.For ISSR analysis,7 primers were identified with polymorphism among the entries.In total 96 bands were produced,of which 44 bands were polymorphic.Percentage of polymorphic bands was 45.8%.Pairwise similarity coefficients combining both RAPD and ISSR markers ranged between 0.881 and 0.979,with an average of 0.933.Clustering of genotypes had some differences when RAPD-and ISSR-derived dendrograms were compared.The dendrogram combining both two markers was more comparable to the information on pedigree.The selection pressure had great effects on the genetic relationships between varieties.The fact that the introduced varieties from abroad were not separated from the developed varieties in China implied that the genetic relationships based on the molecular marker data did not cor-(respond)well with the geographic sources.