A simple and efficient protocol for isolating genomic DNA from leaves of Selaginella spp. (S. delicatula, S. repanda, S. bryopteris, S. plana, S. monospora) was developed, involving a modified CTAB protocol of Rogers and Benedich (1994). Increasing the incubation time with the precipitation buffer (1X CTAB) from 1–3 hours to 12–14 hours helped achieve higher quantity genomic DNA from the specimens, when compared with DNA extracted by protocols reported by Dellaporta et al. (1983), Murray and Thompson (1980) and Doyle and Doyle (1987). The DNA yield ranged from 846–1836 µg/ml from fresh and herbaria-preserved leaf samples. The DNA samples were found suitable for genetic diversity analysis with Random Amplified Polymorphic DNA (RAPD) markers. Nine random primers (OPA A17, OPB 4, OPB13, OPC 2, OPC 11, OPD 5, OPG 2, OPG 19 and OPK 10) were studied, of which two primers (OPD 5 and OPG 2) yielded reproducible amplification profile of polymorphic fragments.