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The test was designed to assess the toxicity of methyl tert-butyl ether (MTBE) to Chlorella ellipsoidea and Aphanizomenon flos-aquae during 15 d with concentrations of MTBE from high (2.00×104 mg/L) to low (2 mg/L). The results showed that the toxicity was low when the concentration of MTBE was 1.00×104-2.00×104 mg/L (the greatest inhibition of growth-rate was 70%-71%, occurring on day 1-5). Low concentrations (2-500 mg/L) stimulated algal growth up to the greatest effect of 85%-200% when the concentration of MTBE was 50-100 mg/L on day 3-5. The low concentrations may lead to an algal bloom owing to overabundance, which represents an aquatic ecological risk. However, the stimulatory effect occurred only during the day 1-5 and disappeared gradually during the day 13-15. The toxicity of MTBE (72-120 h EC50) is 6.65×103-9.58×103 mg/L for C. ellipsoidea and that is 1.14×104-2.00×104 mg/L for A. spiroides. We found that the toxicity and ecological risk of MTBE for the algal community structure were low. The toxicity was influenced by the duration of the test. We suggest that the duration of the test should not be shorter than half a life-cycle.