The security of the Sulawesi-Sulu Seas is of great importance for the international seafaring community. As a result, lack of adequate cooperation in this area has raised some concerns over the safety and security of navigation in the waterways. This article focuses on Indonesia and the Philippines role in securing the waters and the behaviour of these two countries when it comes to cooperation. It investigates why they have joined a number of cooperation arrangements while rejecting others. Most scholarly works point at sovereignty concern as the main reason underpinning their decision. Rather than focusing solely on sovereignty infringements, this article argues that Indonesia’s and the Philippines’ decisions towards cooperation initiatives are informed by the calculation of (both the sovereignty and implementation) costs and benefits, and the level of their control over the cooperation outcomes.