Abstract: Menadione,atovaquone,buparvaquone,2-hydroxy-1,4-naphthoquinone and 2-acetoxy-1,4-naphthoquinone were selected as the research objects for further study on the toxic mechanism of naphthoquinones to zebrafish.The damages occurred in the liver chromosomes of zebrafish were measured via micronucleus test when they were exposed to these naphthoquinones within 96 hours.Positive results were appeared between all naphthoquinones,and different degrees were existed between different compounds.Menadione has the highest toxicity than other compounds while 2-acetoxy-1,4-naphthoquinone has the lowest toxicity to hepatocyte.And time-response was appeared in all five naphthoquinones.The result showed that the genotoxicity of naphthoquinones compounds should not be ignored.