The utilization of marine resources contributes to economic development, improved human well-being, and social equity. The Philippine archipelago provides aquatic resources found in various coastal, marine and inland waters, which are considered as some of the most productive and diverse habitats in the world. Climate change adversely affects the socio-ecological conditions of marine and coastal ecosystems. The Philippines has been projected to be one of the most vulnerable countries to climate change, which is expected to exacerbate extreme events such as heavy rainfall during typhoons, increase in temperature during summer months, and a longer dry season. Global increase in Harmful Algal Bloom outbreaks, a potential indicator of climate change, has also been reported. This paper will primarily focus on the major Philippine marine ecosystem issues that need to be considered in relation to the country's economic development framework/strategy. Current national initiatives of the Philippines and involvements in regional collaborations relevant to developing decision support systems for the sustainability and management of these marine ecosystems will also be discussed.