IoT application protocols have a vital role to play while designing and building an IoT system. As the application changes, the functionalities that the protocols have to deliver will also change. We plan to build a marine IoT system by installing environmental monitoring stations on fishing vessels. The fishing vessels form a multi-level P2MP infrastructure network, OceanNet, rooted at an onshore base station which is connected to the Internet. OceanNet has been successfully deployed over the Arabian Sea from the sea shore near our campus. The marine IoT system is composed of a sink node based sensor network, gateway device, and an onshore monitoring station. Sensor nodes can respond to the environmental changes in the form of voltage or current. In this work, we present a detailed comparison of Constrained Application Protocol (CoAP), Advanced Message Queuing Protocol (AMQP) and Message Queuing Telemetry Transport Protocol (MQTT) for a marine IoT application scenario.