Over the past two decades, the Government of Indonesia has gradually introduced protectionist policies on controlling mangrove deforestation. The policies indicate the importance of mangroves in the context of global climate change. As mangroves are located in between land and sea, their management falls under many different government authorities. This poses major coordination challenges across line ministries. To improve coordination across sectoral regulatory and institutional frameworks, a National Strategy on Mangrove Ecosystem Management was introduced in 2012 as a stepping stone in achieving an integrated mangrove management. The framework however facing some challenges that need some improvement for effective implementation. This paper discusses some of these regulatory and implementation challenges.