Benthic diatoms from three river catchments across Hainan Island’s five national natural reserves were examined to explore the community structure and spatial distribution patterns. Among the 174 benthic diatom species in 55 genera observed from the 30 sampling sites, the dominant genus is Achnanthes with relative abundance of 52.3%. Cluster analysis and non-metric multidimensional scaling (NMDS) analysis reveal a distinct geographic pattern, which differentiate the western Bawangling, western Jianfengling, the middle Yinggeling and Wuzhishan, and the eastern Diaoluoshan with various characteristic benthic diatom communities. Diatom diversity is the lowest in the western mountain zone but highest in the middle mountain zone. The contrast in benthic diatom community between the western mountains, and the middle and eastern mountains possibly suggests a climate control by southeast Asian monsoon. At most of the 30 study sites, the dominant species are indicators of clean water quality, such as Achnanthidium minutissimum, A. rivulare, Achnanthes subhudsonis, Gomphonema clevei and Navicula cryptotenella; whereas only a few sites contain Gomphonema parvulum and Aulacoseira ambigua, indicators of high levels of nutrients. This indicates that the rivers investigated are in good condition, but one should be cautioned against the eutrophication trend at a few sites with intensified human activities.