The present disclosure pertains to systems and methods for selectively encrypting data flows within a software defined network (SDN). In one embodiment, a communication device may be configured to receive a plurality of unencrypted data packets. The communication device may receive from an SDN controller a criterion used to identify at least one of the unencrypted data flows to be encrypted. Based on the criterion, an encryption subsystem may generate an encrypted data flow the unencrypted data packets based on an encryption key. In some embodiments, the encryption system may parse the packets and encrypt the data payloads without encrypting the routing information associated with the packet. In other embodiments, the encryption subsystem may be configured to encapsulate and encrypt the entire unencrypted data packet. In some embodiments, the encryption subsystem may further be configured to authenticate a sending device and/or to verify the integrity of a message.