Ecotoxicogenomics and ecotoxicoproteomics are integration of genomics and proteomics into ecotoxicology. Ecotoxicogenomics is defined as the study of gene and protein expression in non-target organisms that is important in responses to environmental toxicant exposures. Ecotoxicogenomic tools may provide us with a better mechanistic understanding of ecotoxicology, and they are likely to provide a vital role in ecological risk assessment. Progress in ecotoxicogenomics and ecotoxicoproteomics are discussed in this paper. DNA gene chip and 2D-gel usually used in ecotoxicogenomics and ecotoxicoproteomics are also expounded by examples.