Improvement of wood quality related traits is currently hampered by costly chemical and technological assays and the necessity to wait until the trees are nearly mature to evaluate wood properties. The availability of a vast quantity of genomic data opens now a new avenue to identify early selection criteria based on molecular information and therefore increase selection efficiency. Association mapping is becoming a method of choice to identify QTN (quantitative trait nucleotide) that contribute to complex trait variation. The implementation of this approach requires on the one hand knowledge of the molecular mechanisms underlying trait variation and polymorphism within candidate genes, and on the other hand the availability of phenotypically well characterized genetic material. We are developing this strategy in the frame of the maritime pine breeding program, an economically important forest tree species in the South Western Europe. This poster reviews the results obtained in respect to the pattern of nucleotide diversity for a set of wood quality candidate genes (structural genes of the lignin and cellulose biosynthesis, transcription factors). In addition to the estimation of diversity levels and extent of linkage disequilibrium, this study also provides some clues about compatibility between nucleotide diversity patterns and neutral models of molecular evolution.