Abstract: Key areas identification, zone division and long-term monitoring is the key for establishing of harmful algae blooms (HABs) early warning system.Based on the historical records of HABs in the coastal waters of Hainan Island, severities of HABs events were evaluated by analyzing the comprehensive information of occurrence frequency, scale, damage degree and toxicity of causative species in different areas.Combining the diffusing capacity and nutrient availability with the severities degrees of historical records, high incidence region, prone region and potential region of HABs were identified in the coastal waters of Hainan Island by using GIS tools.Based on susceptible grades, environmental function zoning of coastal water and field data, the key monitoring regions were determined and graded.