The development and application of genomics has been facilitated in a number of fields by the availability of new methodologies and tools, such as high throughput DNA sequencing and complementary DNA (cDNA) microarrays. Genomic tools are already used in research on commercially important fish and shellfish species. Thousands of expressed sequence tags (EST) are now available for some of these species, and the sequencing of complete genomes of tilapia, cod, salmonids, flatfishes, sea bass and Pacific oyster has been proposed. Microarray technology through simultaneous analysis of the expression of thousands of genes allows the identification of candidate genes involved in the function of multiple physiological, morphological and behavioural traits of interests in organisms and populations from different environments. This paper reviews the current development of genomic technologies, and pinpoints their potential beneficial applications as well as implications for fisheries management and aquaculture.