Colorectal cancer is one of the worldwide common malignancies with a high mortality level. The major constituent of natural oil of black seed "Nigella sativa" is Thymoquinone (TQ), which has a magical anti-proliferative activity against colorectal cancer cells. This study evaluates the potential cytotoxic effect of TQ on human colorectal cancer cells (HCT-116). Results showed that TQ cytotoxicity was significantly increased (p< 0.001) in the cell culture containing TQ (HCT-116/TQ+) as compared to controls without TQ (HCT-116/TQ-), where maximum effect reached at 60 μM of TQ. Additionally, expression of three important tumor associated gene studied in parallel (p53, caspase 3 and Bcl-xl genes). Both p53 and caspase 3 genes show significant increase in cell cultures containing TQ (HCT-116/TQ+) than controls without TQ (HCT-116/TQ-). Conversely, Bcl-xL gene show significant decrease. All these observations concluded that thymoquinone (TQ) was cytotoxic towards HCT-116 cells in a dose-dependent manner and induced apoptosis via caspase 3 and p53-dependent pathway.