NASA's Space Communications and Navigation (SCaN) program is integrating its three current agency networks: Space Network (SN), Deep Space Network (DSN), and Near Earth Network (NEN). This effort raises several issues for the network management in the future integrated space networks. First, an integrated network management function, which uses common standards and implementations, is needed to serve as the interface for all SCaN network customers. Second, satellite operations currently use a highly manual approach. The research and development of autonomous operations has been conducted recently but is still at early stage. Third, due to different characteristics of space networks, security management mechanisms and other network management functions that are widely adopted in the traditional networks are not fully suitable to space networks. In addition, several issues related to Bundle Protocol exist and need to be further investigated to enhance the performance of bundle delivery in delay tolerant networks. To address these issues, we propose an innovative Security-Enhanced Autonomous Network Management (SEANM) scheme for reliable communication in space networking, which allows the system to adaptively reconfigure its network elements based upon awareness of network conditions, policies, and mission requirements.