An ideal assessment would examine conservation importance at both the species level (examining endemics and total species) and the ecosystem level (examining unique habitats). This analysis considers only total species count for one taxonomic group -- coral fish species -- and not the total count of all species. In choosing priorities for protection, many planners also consider nonbiological criteria, such as identifying sites to protect on the basis of economic and social values.

One major consideration in identifying conservation priorities is the degree to which sites are already protected as parks and reserves. Unfortunately, the data and maps used for this analysis were too coarse to allow detailed examination of protected area gaps (existing marine protected area data are also incomplete and/or are not adequately spatially referenced). The map -- "...and most areas with high reef fish species diversity are not protected" -- provides an idea of some of the possible gaps in protection in Southeast Asia. Many areas in the Philippines and Indonesia have high species diversity, are highly threatened, and are not protected.