In order to understand the cause of a fish killing accident occurred in a fish pond in Guangzhou in September 2006, fish acute toxicity test by Brachydanio rerio and root tip micronucleus test by Vicia faba were conducted with the contaminated water. 96h LC₅₀ values of water samples from a chemical factory discharge area and the central pond were 1.69%, 23.95%, respectively; micronucleus frequencies were 27.8‰, 13.7‰ respectively. COD, BOD, oils, NH₃-N, TP of both water samples were over-standard. The result showed that effluent of the chemical factory is the main cause of fish kills. Moreover, the effluent significantly enhanced the micronucleus frequencies, and increased the risk of potential mutagenicity.