The KM3NeT Collaboration is installing two neutrino telescopes at the bottom of the Mediterranean Sea, ARCA and ORCA. These detectors are built in the form of very large 3D arrays of photomultipliers (PMTs) detecting the Cherenkov light induced by relativist particles propagating in the sea water. The PMTs are installed inside pressure-resistant glass spheres, the Digital Optical Modules (DOMs), each containing 31 PMTs together with the electronics for data taking and communication. Eighteen DOMs and a base module are comprised in a detection unit (DU), a structure standing on the sea bottom with a height of almost 700 m for ARCA (200 m for ORCA). For optimal performance of the detectors, a good synchronization of all parts of the detectors is required. The data acquisition system of KM3NeT has been designed based on the White Rabbit (WR) protocol. In a first phase of construction of the detectors, this has been developed in a tailored design based on a “broadcast” approach: in such scheme, the communications from the shore station to the detectors is performed by distributing the same data stream to all underwater nodes, while in the opposite path each single DOM sends data to shore through its own communication channel. For the next phase of construction, a new system has been developed, based on the standard WR protocol. This approach has some significant advantages, in terms of maintainability and scalability of the system, which are obtained with a non-negligible cost, however, since it became necessary to design tailored WR components which
would meet the KM3NeT requirements and to modify the full design of the apparatus consequently. In this paper we will present and compare these two DAQ system designs.