Protected areas in Thailand were first established 40 years ago. The total area of existing protected areas covers 18.2% of the country's land area and the Class 1 Watershed, another form of protection, encompasses 18.1%. The government of Thailand intends to increase protected area systems to 25% of the country in 2006 and 30% in 2016. There are always questions arising about how much is enough protected areas to effectively protect biodiversity. The objective of this article is to assess the representation of ecosystems in the protected area network. This article also recommends which underrepresented ecosystems should be added to fill the gaps in representativeness. The research applies a gap analysis and a comparison index to assess the representation of ecosystems within the protected area network. The spatial analyses were applied to measure three aspects of representativeness, namely forest type, altitude, and natural land system. The analyses indicate that the existing protected area system covers 24.4% of the country's land area, nearly meeting the 25% target proposed by the National Forest Policy; and 83.8% of these areas are under forest cover. Most protected areas are situated in high altitudes, where biological diversity is less than in lowlands. Mangrove forest and riparian floodplain are extremely underrepresented in the existing system. Peat swamp forest, dry dipterocarp forest, and beach forest are relatively well represented. In addition, these five ecosystems are threatened by human pressures and natural disasters; therefore, they should be targeted as high priorities for the selection of new reserves. Future research should incorporate aquatic and marine ecosystems, as well as animal distributions, which were not included in this research due to data unavailabilities.