Since its establishment in 2007, MERC has formed positive working relationships, ranging from individuals (such as student researchers and volunteers teaming up with MERC employees in the field), private organizations (through visits under their Corporate Social Responsibility programmes), institutions (academic professionals in marine conservation and other related fields), non-governmental organizations (collaborating in joint awareness programmes either on-site or off-site) and government organizations (such as with Department of Fisheries Sabah on enforcement issues pertaining to Giant Clams and other marine species).

A key partnership formed by MERC is with Borneo Eco Fish whom MERC works closely with in its aquaculture efforts to reduce pressure on wild fish resources.