Backround: The RAPD- and ISSR-PCR techniques are offering an insight into the detecting the genotoxicity of Gentiana extracts. Objective: It is aimed with the present study, to detect the genotoxicity of methanol extracts of ten Turkish Gentiana L. taxa on germinated Allium cepa L. root tips. Methods: RAPD- and ISSR-PCR techniques were used for detection of genotoxicity of Gentiana extracts. Results: Four RAPD and three ISSR primers produced the reproducible polymorphic and monomorphic banding patterns among 10 RAPD and 10 ISSR primers for all DNA samples. It is not any serious alteration along with band intensity change, the disappearance of the bands, and appearance of the new bands in the band profiles amplified from the Gentiana extracts-treated genomic DNA sample of A. cepa. The most efficient results were obtained by RAPD-P9 and ISSR-1 primer among the seven productive primers. Discussion: It is not observed any variation in the RAPD- and ISSR-PCR band profiles in time and concentration-dependent manner. Conclusion: It is determined that the three different concentrations of Gentiana extracts did not interact with the A. cepa DNA.