Interest in bivalve genomics has emerged during the last decade, owing to the importance of these organisms in aquaculture and fisheries and to their role in marine environmental science. Knowledge of bivalve genome structure, function and evolution resulting from 20th century "single gene" approaches is limited, but genomic technologies are called to dramatically increase it. Research based on linkage maps, transcriptomics and proteomics is being carried out to study the genetic and molecular bases of traits of interest in bivalve farming industry, mainly disease susceptibility, tolerance to environmental stress, and growth. The Pacific oyster (Crassostrea gigas) is now the focus of an international genome-sequencing consortium. The use of bivalves in pollution monitoring has prompted the genomic study of the cell and organism responses to xenobiotics, which should expand into the field of phytoplankton toxins. Future work should also pay more attention to the larval stages, and to basic processes such as growth, sex-determination, and gonad development. (c) 2006 Elsevier B.V All rights reserved.