Oceans are homes of marine biodiversity, which includes fish and their ecosystems essential for human well-being. Indonesia and Australia are both rich in marine biodiversity. However, there are strong indications that marine biodiversity has been deteriorating in Indonesia, Australia and globally. Loss of marine diversity is largely as a result of conflicting uses of coastal habitats, land-based marine pollution, destructive fishing practices, IUU Fishing, overfishing, invasive alien marine species, and climate change. This article examines marine biodiversity laws in Indonesia and Australia, and In particular it examines the implementation of the Convention on Biological Diversity, 1992 (CBD) in domestic legal framework in conservation and sustainable use marine biodiversity. The article concludes that laws in Indonesia and Australia are in place to conserve and sustainably use marine biodiversity but that there are many challenges to effective implementation of the legal framework in both countries. While in Indonesia the prominent challenge is integrating marine conservation and food security, in Australia one of the significant challenges is to tackle climate change impacts on coral reefs in world heritage sites.