Systems and methods are disclosed for application identification and dynamic signature generation for managing network communication systems. Communication sessions and related packet flows are monitored within a network communication system. Application level information is extracted from session packets by unpacking one or more communication protocols associated with the network packets to obtain application level information encapsulated within the network packets. The extracted application level information is compared to a database of known application signatures in order to identify known applications. For unknown applications, the application level information is used to generate new dynamic application signatures. The application level information can also be used to identify and access external network-accessible resources to obtain additional identification information for the unknown application. Identification information for the newly detected application can then be provided to a user along with flow control options for the newly detected application.