Autonomous vehicular clouds, as the combination of cloud computing and conventional vehicular ad hoc networks, will provide abundant resources and services by sharing under-utilized resources of future high-end vehicles such as computing power, storage and internet connectivity. Autonomous vehicular clouds will have significant impact if widely implemented in the intelligent transportation system. However, security and privacy issues are still big challenges in autonomous vehicular clouds. In this paper, after analyzing the particularity of autonomous vehicular clouds, we implement a two-layered architecture, in which vehicles are self-organized without the help of roadside units. Then based on the architecture, we put forward an effective key management protocol to distribute a group key efficiently and also provide the authentication and confidentiality that lots of current secure schemes ignore. In addition, according to the different scenarios and security levels we categorize the way of message transmitting into three kinds. At last, with performance evaluations, the proposed protocol can perform more efficiently than other well-known available schemes.