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Some implementations of MQTT (such as IBM WebSphere MQ and Mosquitto 1+) support SSL/TLS encryption as included features.
Additionally, SSL/TLS tunnels, SSH tunnels or traditional VPN protocols like IPSec may be used to encrypt the communications between the client and the broker.
Encryption may also be applied outside of MQTT, on the data itself - in the payload of the messages, as a feature of the application.