Comparative QTL mapping for adaptive traits among populations and species can lead to the identification of genomic regions conserved over a long evolutionary period and therefore potentially harboring genes of great importance for adaptive processes. At the same time, non-conserved QTLs could be responsible for local adaptation or interspecific differentiation. The availability of Populus as a model system for tree and woody perennial plant biology has largely been driven by the rapid development of genomic and molecular biology resources for this genus, culminating in the completion of a draft sequence of the Populus trichocarpa (black cottonwood) genome. Numerous genetic maps are available in different Populus and Salix species and QTLs for adaptive traits (such as phenology and disease resistance) and sex have been mapped. All these maps showed a very good synteny with the P. trichocarpa genome; however, very few markers are currently shared between these maps. The objective of our study is to take advantage of the information on the P. trichocarpa genome sequence to perform QTL projection and identify candidate genes. Genetic maps from 7 pedigrees, belonging to 4 Populus spp. were aligned with the help of common simple sequence repeat and gene markers. Three additional published maps from Salix spp. were partially anchored to the P. trichocarpa genome sequence. QTL meta-analysis and projection of QTL intervals on the genome sequence were performed when sufficient genome anchoring markers were available. These analyses allowed identifying large genome regions containing several hundred of candidate genes. Thanks to the availability of biological knowledge accumulated in public data bases (e.g. Gene Ontology) and high-throughput enrichment tools, we have explored these gene lists by functional analysis if QTL regions are statistically enriched in some functional categories compared to the entire genome.