||The development of fish and shellfish farming is facing several challenges linked to the infancy of the industry: i.e. domestication, genetic improvement of disease resistance, genetic improvement of feed efficiency to fish meal and fish oil substitution by vegetal products, development of adapted vaccines, supply of fry or spat at high quality and high robustness, adaptation to environmental change, production of healthy, high quality consumer products and limitation of environmental impact of the activity and escapees. Over recent years, the EU and individual countries have supported the development of genomic tools for some aquaculture species (e.g. rainbow trout, sea bass, sea bream, turbot pacific oyster, Atlantic salmon). New perspectives arise with the development of genome sequencing, genetic and physical maps and genetic markers. Also, new high-throughput technologies will reduce the cost of genotyping and give access to large amounts of genetic information, useful in several applications: such as reproduction, breeding programs and new traits (disease resistance, quality, etc...), development of new vaccines or new drugs or prophylaxy practices to improve broodstock sanitary status and animal health, feed formulations and substitutions and feeding practices, etc... In this context, this presentation provides the state of the art on "Genome mapping in shellfish aquaculture species" focusing on oysters and mussels to aquaculture professionals from Southern and Eastern European and Mediterranean countries involved in rainbow trout, sea bass, sea bream and oyster production.