As a major natural reservoir of influenza virus and an important food source, the duck is of great biological interest, e.g. in the area of host-pathogen interactions. Recently, preliminary genetic and cytogenetic maps of the duck have become available, providing for the first time a glimpse at a comparative map between the duck and chicken. These genetic tools have been used to detect QTLs related to duck growth, carcass and meat quality traits. However, molecular genetic research in the duck is only in its infancy. In the future we can expect the development of new duck resources, including a high-density genetic map, detailed comparative maps with the chicken and other vertebrates - and given the pace of genomics, possibly a genome sequence. These new resources will be used to evaluate the genetic diversity of global duck breeds, to define genetic markers to increase the quantity and quality of egg and meat products, and to aid in the battle against infectious diseases, such as avian influenza.