Physical layer security (PHY-security) takes the advantages of channel randomness nature of transmission media to achieve communication confidentiality and authentication. Wiretap coding and signal processing technologies are expected to play vital roles in this new security mechanism. PHY-security has attracted a lot of attention due to its unique features and the fact that our daily life relies heavily on wireless communications for sensitive and private information transmissions. Compared to conventional cryptography that works to ensure all involved entities to load proper and authenticated cryptographic information, PHY-security technologies perform security functions without considering about how those security protocols are executed. In other words, it does not require to implement any extra security schemes or algorithms on other layers above the physical layer. This survey introduces the fundamental theories of PHY-security, covering confidentiality and authentication, and provides an overview on the state-of-the-art works on PHY-security technologies that can provide secure communications in wireless systems, along with the discussions on challenges and their proposed solutions. Furthermore, at the end of this paper, the open issues are identified as our future research directions.