The sustained mass production of alevins in finfish aquaculture requires a deep understanding of the biological processes controlling gametogenesis, which ultimately will determine the quality of eggs and sperm. Functional genomics and proteomics technologies have been recently developed, expanding the scope of biological investigation from studying single genes or proteins to studying potentially all genes and proteins at once in a systematic manner The application of these methods in aquaculture is still in its infancy, especially with regard to the study of fish reproduction, but in the near future its impact is envisaged because of their potential to uncover the complex genetic control of gamete formation. Here, we review recent studies employing high-throughput genomics and proteomics approaches that have been carried out to investigate the global pattern of gene and protein expression during finfish gametogenesis. The results of these studies have already identified a number of novel genes, maternal molecules, and proteins that may be essential during spermatogenesis, oogenesis, and early embryogenesis, thus greatly contributing to our current knowledge of the molecular mechanisms underlying egg and sperm formation. The full potential of genomics to uncover the molecular basis of fish gametogenesis is about to be unleashed with the sequencing of the genome and transcriptome of additional species and the development of methods to elucidate gene function.