Genetic relationship among 21 Rubus ellipticus accessions, collected from different sites in Himachal Pradesh and Uttrakhand, was evaluated by using 20 Expressed sequence tag-Simple sequence repeats and 35 Inter simple sequence repeats. The ESR-SSRs were designed by extracting seven EST sequences from Rubus ellipticus and 3184 sequences from other species of Rubus such as Rubus ulmifolius and Rubus ideaus obtained from national center for biotechnology information. The ESTs containing simple sequence repeat motifs were extracted using SSR Identification Tool and 20 primers were designed with primer 3 software. These EST-SSR primers generated 40 polymorphic bands, whereas ISSRs generated 173 polymorphic bands. Polymorphic information content (PIC) for ISSRs was higher (0.886) than that of EST-SSRs (0.667). Effective multiplex ratio and marker index values for EST-SSRs were 1.09 and 0.62 and, for ISSRs, these values were 8.24 and 5.83, respectively, which were used to develop dendrograms. With EST-SSR two cluster ‘A’contained 19 collections whereas cluster ‘B’contained two collections with maximum similarity of 67%. For ISSRs, 21 collections were divided into two cluster, ie, cluster ‘C’, which contained six collections and cluster ‘D’that contained 15 collections with maximum similarity of 56%. Thus EST-SSRs and ISSRs used in the present study revealed a high level of polymorphism in the 21 collections of Rubus ellipticus, revealing their efficiency for diversity analysis studies.