In 2016, the rural municipality of Toboso, Philippines, underwent its first assessment of coastal ecosystem health and diversity, as part of an effort by the municipal government and stakeholders to implement a Marine Protected Area. The present paper provides an in-depth comparison between an area currently proposed by the municipal body (PMPA) and an alternate area (AMPA) first proposed in 2016. Both areas show extensive differences across the entire data range, with the AMPA hosting a far greater total diversity of species, diversity of fish and corals and total hard coral cover. Additionally, the AMPA site supported greater numbers of ecologically and economically important fish and invertebrate fauna, though still showing indications of a heavily overfished ecosystem. Surveys were also carried out in local fish markets to assess the role of local coral reefs in the overall fishery at Toboso. These findings increase the total number of faunal taxa recorded from Toboso from 435 species to 589, and 73 species of marine associated flora. Also documented is the first record in the Philippines of the skeleton forming octocoral genus Nanipora.
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