The biodiversity of East to Southeast (E–SE) Asian waters is rapidly declining because of anthropogenic effects ranging from local environmental pressures to global warming. To improve marine biodiversity, the Aichi Biodiversity Targets were adopted in 2010. The recommendation of the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA), encourages application of the ecologically or biologically significant area (EBSA) process to identify areas for conservation. However, there are few examples of the use of EBSA criteria to evaluate entire oceans. In this article, seven criteria are numerically evaluated to identify important marine areas (EBSA candidates) in the E–SE Asia region. The discussion includes 1) the possibility of EBSA criteria quantification throughout the E–SE Asia oceans and the suitability of the indices selected; 2) optimal integration methods for criteria, and the relationships between the criteria and data robustness and completeness; and; 3) a comparison of the EBSA candidates identified and existing registered areas for the purpose of conservation, such as marine protected areas (MPAs). Most of the EBSA criteria could be quantitatively evaluated throughout the Asia-Pacific region. However, three criteria in particular showed a substantial lack of data. Our methodological comparison showed that complementarity analysis performed better than summation because it considered criteria that were evaluated only in limited areas. Most of the difference between present-day registered areas and our results for EBSAs resulted from a lack of data and differences in philosophy for the selection of indices.