Colchicine has been widely used to induce polyploidy in plants, but the methods of treatment, colchicine concentrations and time of exposure vary from one species of interest to another. The purpose of this study was to determine which colchicine treatment method and concentration is the most suitable for basil, and if alterations in the morpho-anatomy of treated plants and variations in assimilatory pigments contents could indicate changes in the quantity of genetic material in plant tissues. These changes could precede flow cytometry or other cytogenetic analyses and were also observed in order to compare the responses of two basil varieties to colchicine treatment. The experimental design focused on testing different methods of treatment with colchicine (on seeds and on caulinar apex) based on the methods used by Omidbaigi et al. (2010) with some adaptations. For morphological observations, leaves from individuals of each variant were photographed and Scanning Electron Microscopy was also employed. Transversal sections of the stems of treated plants were made for anatomical observations, and chlorophyll pigments contents were determined according to the method used by Sumanta et al. (2014). Statistical analyses on stomata size and density, and on tector and secretory hairs density were made using one-way ANOVA. The results of the experiment show different responses to colchicine treatment in both target varieties, with profound changes in the plants’ morphology and anatomy, and variations in chlorophyll pigments content. Overall, the treatment on caulinar apex showed better results on both varieties. This study shows that colchicine does not induce biological effects on all treated basil plants, therefore the method should be further explored. We obtained diploid and what we observed to be some potentially mixoploid plants. Furthermore, the varieties had different responses to colchicine treatment. These observations could pave the way for differential colchicine treatment methods based on the variety of basil used in the respective studies.