Amiprophos-methyl (APM) and colchicine (COL) are therapeutic agents and are also used in plant science. Cell cycle synchronization (CCS) is mediated by hydroxyurea (HU) and APM. The genotoxic effects of APM are unclear. In order to assess the genotoxicity of APM separately and with HU and then compare it with COL, we treated 2-day-old barley (Hordeum vulgare 'Bornova-92') seedlings with 8 µM APM for 2 h, 1.25 mM COL for 18 h, or 1.25 mM HU for 18 h and 4 µM APM for 2 h, with a final ice-cold water incubation. Following treatment, seedlings were recovered without any substance for 2 days. Genomic DNA samples were analyzed by random amplified polymorphic DNA, inter-simple sequence repeat, and inter-retrotransposon amplified polymorphisms. Polypeptide profiles were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Mean genomic stability (GTS) values at the end of APM, COL, and CCS treatments were 83.6%, 83%, and 82.3%, respectively. Mean GTS values after recovery from APM, COL, and CCS treatments were 78.5%, 83.9%, and 78.7%, respectively. APM treatment resulted in altered polypeptide profiles during both treatment and recovery. The genotoxicity of APM and COL was similar, while the genotoxic effects of APM continued after removal. Only COL treatment caused retrotransposon activation. APM treatment caused appearance of new polypeptides, which continued after the removal of APM. Although the microtubule inhibitory effect of APM has been reported to be reversible, APM may cause genotoxic effects on plants, and the molecular effects of APM may not be reversible.