Standard Cryptographic Protocol
Adversaries may explicitly employ a known encryption algorithm to conceal command and control traffic rather than relying on any inherent protections provided by a communication protocol. Despite the use of a secure algorithm, these implementations may be vulnerable to reverse engineering if necessary secret keys are encoded and/or generated within malware samples/configuration files.
Some versions of UPPERCUT have used the hard-coded string "this is the encrypt key" for Blowfish encryption when communicating with a C2. Later versions have hard-coded keys uniquely for each C2 address.
Network intrusion detection and prevention systems that use network signatures to identify traffic for specific adversary malware can be used to mitigate activity at the network level. Use of encryption protocols may make typical network-based C2 detection more difficult due to a reduced ability to signature the traffic. Prior knowledge of adversary C2 infrastructure may be useful for domain and IP address blocking, but will likely not be an effective long-term solution because adversaries can change infrastructure often. 
SSL/TLS inspection is one way of detecting command and control traffic within some encrypted communication channels.  SSL/TLS inspection does come with certain risks that should be considered before implementing to avoid potential security issues such as incomplete certificate validation. 
If malware uses encryption with symmetric keys, it may be possible to obtain the algorithm and key from samples and use them to decode network traffic to detect malware communications signatures. 
In general, analyze network data for uncommon data flows (e.g., a client sending significantly more data than it receives from a server). Processes utilizing the network that do not normally have network communication or have never been seen before are suspicious. Analyze packet contents to detect communications that do not follow the expected protocol behavior for the port that is being used. 
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