Methods and systems for software obfuscation are disclosed. In one exemplary embodiment, the obfuscation includes integrating the checker code with product code to form integrated code. The product code includes a first portion that provides desired functionalities to a software product, while the checker code includes a second portion that protects the product code from unlicensed use. A generated pseudorandom value is used to select one or more instruction sequences of the integrated code. Following the selection, the instruction sequences may be replaced with equivalent instruction sequences to form a new integrated code. Alternatively, the original integrated code is transformed into new integrated code when the selected instruction sequences are optimized. Additionally, the new integrated code may be compared to the original integrated code by generating output states from each integrated code. The new integrated code is functionally equivalent to the original integrated code if the respective output states match.