White and black poplars (Populus alba L. and P. nigra L.) are native to Eurasia and their genetic diversity for their growth potential and stress-adaptive mechanisms is underexploited. A better knowledge of their genome will allow more effective protection and use of critical genetic resources for breeding programs. The main objective of this study was to find quantitative trait loci (QTL) associated with adaptive traits and compare the P. nigra and P. alba maps among them and with the genome sequence of P. trichocarpa. For that, four parental genotypes were selected from contrasting natural Italian populations and crossed to generate two F1 mapping pedigrees. Highly informative genetic maps were constructed based on amplification fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. These maps showed good overall colinearity to each other and a good synteny between the two species for the very high number of common markers. Both species allowed a complete alignment with the 19 haploid chromosomes of the P. trichocarpa genome sequence. Comparative analysis among maps of P. alba and P. nigra, and the P. trichocarpa genome sequence revealed a putative region of chromosome translocation between linkage groups II and XIV in P. nigra. Such comparative mapping is a crucial step to gain insight into the way in which genome structure and function differ among Populus species. Genetic mapping of QTL have also proven its utility in the identification of genomic regions associated with the expression of adaptive traits, such as growth, crown architecture, and phenology. The identification of QTL intervals on the four maps allowed us to perform QTL projection on the P. trichocarpa genome sequence, and to identify genome regions including candidate genes for adaptive processes. This approach will greatly facilitate the study of the genomics of Populus and how it can be exploited in applied breeding programs. Selection based on molecular markers tightly linked to traits of commercial importance could ultimately prove useful as a powerful adjunct to conventional approaches in Populus improvement programs.