In the current study, it is aimed to investigate the toxic effects of a widely used herbicide Roundup containing active ingredient glyphosate on cucumber (Cucumis sativus) by cytological and molecular investigation. Three different concentrations (0.6%, 1.2% and 2.4%) of Roundup were applied to cucumber for 48 and 72 hours. At the end of the application procedure, the germination percentage, mean root length, mitotic frequency and mitotic abnormalities, RAPD profiles and Genomic template stability (GTS) were determined in root apical meristematic cells. For RAPD PCR analysis 10 RAPD primers were used, 8 of them produced band patterns and it was found that 5 RAPD primers among them produced unique polymorphic band patterns and subsequently were used to produce a total of 24 bands. Observed percentage of polymorphism was 26%. The changes in RAPD profiles after Roundup treatment was included variations as gain and/or loss of bands compared with the control group. Genomic template stability changed in RAPD profiles at various Roundup concentrations.