The Internet of Things, i.e., IoT system or application, succeeds considerably depending on the communication standards and choice and implementation of the protocols. The selection of proper communication standards and an efficient protocol used for communication and for establishing connectivity in IOT is difficult because of the heterogeneity and resource restrictions of IOT devices. There are protocols designed and adopted as well for the purpose of messaging in the field of IoT. There is no categorical communication protocol designed that is able to cooperate all communication (messaging) use cases and justify the complete necessities of Internet of Things (IoT) systems. Hence, it becomes difficult to apprehend the protocols of the application layer specifically utilized for messaging and/or communication purpose in IoT systems. This paper delivers a relative study of the Constrained Application Protocol (CoAP), Hypertext Transfer Protocol (HTTP), and Message Queuing Telemetry Transport (MQTT) messaging protocols including their security.