Twenty one different varieties of chrysanthemum were selected for the characterization of all species that will help in the varietal selection programme for commercial breeding. All chrysanthemum varieties were analyzed by using two parameters e.g. morphological and molecular parameters. After molecular characterization phylogenetic relationship among all selected varieties was accessed through computer based software DNAMAN that allows the breeder to choose the parentage which is most reliable for the selection of clones before breeding activities.For morphological characterization the plant height, flower type, colour, leaf shape, size and leaf arrangement was studied. The plant height ranges form 35-117 cm. In all varieties the leaf arrangement was spiral but the leaf size varies from one variety to other. Single and double chrysanthemum were classified into different groups. For molecular characterization total 15 RAPD primers were screened to assess the genetic diversity of all the selected chrysanthemum varieties.The sequence similarity was 79.55 with 33% polymorphism in selected chrysanthemum.