Explants from bulb scales of Lilium tsingtauense Gilg. were cultured on MS medium with different exogenous plant growth regulators. M1 medium (MS + 0.1 mg l^-1 NAA + 2.0 mg l^-1 BA) produced 52 in vitro plantlets regenerated from adventitious shoots; M2 medium (MS + 0.1 mg l^-1 NAA + 2.0 mg l^-1 TDZ) had just 2 in vitro plantlets and M3 medium (MS + 2.0 mg l^-1 BA+2.0 mg l^-1 2,4-D) had none. These in vitro plantlets were examined for the presence of somaclonal variation by random amplified polymorphic DNA (RAPD) markers and inter simple sequence repeat (ISSR) markers. Twelve RAPD primers yielded 36 polymorphic bands and 10 ISSR primers produced 38 polymorphic bands, showing 36.73% and 43.18% polymorphism, respectively. Dendrograms based on polymorphism generated 70.8% (RAPD) and 73.7% (ISSR) similarity, indicating a low similarity index between each micropropagated plant and the donor plant. Both RAPD and ISSR markers were able to detect genetic variability during the regeneration process, but there was better reproducibility with ISSR markers.