In view of the high level of morphological diversity in fern species, assessment of genetic variation among 19 fern species was evaluated using ten inter simple sequence repeat (ISSR) markers. The results suggested that the ISSR markers produced much better reproducible bands and were more efficient in grouping fern species. ISSR fragments generated 29 to 87 bands per primer. A total of 281 polymorphic bands generated 34.48 to 66.66 per cent polymorphism per primer. All germplasm were clearly differentiated by their ISSR fingerprints. The similarity coefficient on ISSR profiles were subjected to UPGMA cluster analysis between the species was within the range from 1.00 to 25 per cent. The dendrogram generated by ISSR markers revealed two major clusters, indicating that fern species have distributed based on frond shape, frond type, type of rhizome, habitat, stipe colour, texture, sori position. This is the first report in ferns genetic diversity estimation and clustering by using ISSRs.