In this study, five samples from ferns plants namely Asplenium ceterach, Asplenium aethiopicum, Asplenium trichomanes, Cheilanthes pteridioides, Adiantum capillus-veneris were collected from El Souda Mountains, Abha area, Saudi Arabia. The DNA was extracted from fresh leaves and five random amplified polymorphic DNA (RAPD) markers, five inter-simple sequence repeat (ISSR) markers were used to investigate the genetic variations of the investigated plants. ISSR markers produced 39.0 bands recording 7.5 bands per marker with a polymorphism 60.57% and the highest genetic similarity (82.05%) was found between A. ceterach and A. aethiopicum, while the lowest similarity (28.21%) between A. trichomanes and C. pteridioides. RAPD markers produced 45.0 bands with a polymorphism 77.81% and the highest similarity (61.70%) was between A. aethiopicum and A. ceterach and also between C. pteridioides and A. capillus-veneris while the lowest similarity value (36.71%) between A. capillus-veneris and A. aethiopicum. Summation ISSR, RAPD primers provided the highest similarity value (70.93%) that was found between A. aethiopicum and A. trichomanes, while the lowest similarity value (34.88%) was between C. pteridioides and A. trichomanes. In conclusion, applied biomarkers including RAPD, ISSR showed varied capability to distinguish among the genotypes of ferns plants.