With the rapid development of the internet, copying a digital document is so easy and economically affordable that digital piracy is rampant. As a result, software protection has become a vital issue in current computer industry and a hot research topic.
Software watermarking and obfuscation are techniques to protect software from unauthorized access, modification, and tampering. While software watermarking tries to insert a secret message called software watermark into the software program as evidence of ownership, software obfuscation translates software into a semantically-equivalent one that is hard for attackers to analyze. In this thesis, firstly, we present a survey of software watermarking and obfuscation. Then we formalize two important concepts in software watermarking: extraction and recognition and we use a concrete software watermarking algorithm to illustrate issues in these two concepts. We develop a technique called the homomorphic functions through residue numbers to obfuscate variables and data structures in software programs. Lastly, we explore the complexity issues in software watermarking and obfuscation.