We report the construction of a medium-high density genetic linkage map for Atlantic halibut (Hippoglossus hippoglossus), generated using two maternal half-sib families (n=91). Spanning 24 linkage groups (2n=48), there are 602 unique markers including 256 microsatellites and 346 AFLPs, with an average spacing of <4.5cM between adjacent markers. Microsatellite markers were derived from several sources: 121 were from an Atlantic halibut genomic library enriched for (GT)n sequences, 72 were derived from microsatellites in public databases from other pleuronectid species, and 63 were identified in halibut ESTs. The latter group has allowed us to begin to locate specific genes on the map. Approximate centromere locations have been estimated for each linkage group by genotyping selected microsatellites in gynogenetic offspring, allowing us to relate the linkage map to the physical morphology of the chromosome. As expected, the overall rate of recombination is higher (2:1) in the homogametic females; however recombination in the males is greater toward the distal ends of linkage groups. A comparison with the other Pleuronectid linkage maps indicates some degree of conservation; however major chromosomal rearrangements are evident. Morphometric data was collected for each experimental family to identify potential quantitative trait loci (QTL) associated with pigmentation, body size (length, width, weight) and metamorphosis (eye migration, myotome height). A genetic map and the identification of markers associated with traits of economic importance will allow the Atlantic halibut industry to make significant production gains through marker assisted selection and broodstock enhancement.