The various project components of MLRP are implemented in collaboration with other sister Institutes of MoES and CSIR Institutes working in the field. Following are the major Institutes which are associated with CMLRE in implementing the MLR.

1. Indian National Centre for Ocean Information Services
2. National Centre for Coastal Research, Chennai
3. National Institute of Oceanography-Regional centre, Kochi

In addition to this, CMLRE is in collaboration with the following Centres/Institutes through Memorandum of Understanding (MoU) which allows collaborative surveys and research activities in the various field of Marine Biodiversity.

1. Zoological Survey of India (ZSI)
2. Central Marine Fisheries Research Institute (CMFRI), ICAR
3. National Bureau of Fishery Genetics Research (NBFGR), Kochi