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Fishery is an important industry in China as well as in the rest of the world, and it provides a human food resource containing high-quality protein. Best practice in aquaculture requires a full understanding of the genomic controls and transcriptional profiles of cultured fish species. Improvements in aquaculture can be made by regulation of the expression of functional genes. Microarray technology is a powerful tool for rapid screening of genes or transcriptional profiles in a particular fish or for a particular economic character; for example, genes that are related to growth and disease control in the fish. This review provides a brief introduction to micro-array technology and its methods and applications, together with a discussion of the achievements in fish biology that have resulted from this technology.