Abstract: The cluster analysis of 28 tobacco accessions was assessed using IRAP and ISSR molecular methods.The results based on these two methods were compared.The results were as follow:(1) 214 bands were produced by IRAP,of which 187 bands were polymorphic,and the percentage of polymorphic bands was 87.4%.The 28 accessions could be classified into three groups at the level of L₁=0.495.The third group could be classified into 3 subgroups and 3 unique types at L₂=0.34.(2) 334 bands were produced by ISSR,of which 250 bands were polymorphic,and the percentage of polymorphic bands was 75%.The 28 tobacco accessions could be classified into two groups and 2 unique types(Coker176,BaSmaUovina) at the level of L₁ =0.41.The first group(Ⅰ) included two accessions from America(RG11 and K730),and other 24 accessions were included in the second class(Ⅱ).(3) The correlation coefficient between IRAP and ISSR analyses was 0.823(_r0.01=0.478),which indicated these two methods were both fit for the study of genetic diversity in tobacco.But IRAP technique had higher GD(genetic dissimilarity coefficient),better stability,and higher polymorphic than ISSR method.The genetic diversity and relationship of tobacco germplasm could be distinguished more easily by IRAP.