The present investigation was carried out to evaluate the effects of NaCl stress on genetic stability of lines of Ocimum tenuiflorum L. using RAPD markers. For genetic characterization of controlled and NaCl stressed plants, the extracted DNAs were subjected to RAPD markers, using PCR amplification. For this purpose a total of seven primers viz, OPH_01_F, OPH_01_R, OPH_01_RC, OPI_05_R, OPI_05_RC, OPG_10 and OPC_06 were used. PCR amplification was followed by gel electrophoresis (1.2% agarose gel) and visualized by UV light, which revealed the presence of monomorphic and polymorphic bands in the amplified products. During this analysis, two primers (OPH_01_F and OPH_01_RC) produced a total of 10 bands. Six of the bands were monomorphic i.e. 02 with the control plant, 02 with the 25mM salt stressed plant and 02 with the 50mM salt stressed plants. While with 75mM and 100mM salt stressed plants polymorphic bands were observed showing genetic variation. Profiles generated by the third primer i.e. OPI_05_R showed 4 monomorphic bands with control and NaCl stressed O. tenuiflorum L. While, 100mM salt stressed plant showed total loss of bands. In addition, the expression level of control plant was brighter than the salt stressed plants. The expression level was gradually decreased with an increase in NaCl concentration. These results suggested that increase in salt concentration had a damaging effect on genetic stability of O. tenuiflorum L., which in turn affected the morphology and physiology of plant. The present piece of work also highlights the importance of salt stress as biomarker.