DNA polymorphism of 9 transcription factors putatively involved in wood formation was studied in 6 Pinus pinaster natural populations from the French Atlantic coast. No differentiation was detected between populations, in line with the hypothesis of a large, unstructured meta-population. We tested whether patterns of diversity at each gene departed from the neutral model expectations. HDZ31, LIM2 and Myb1 transcription factors showed a significant excess of intermediate frequency alleles (positive Tajima’s D and Fu’s Fs) and low haplotypic diversities, suggesting balanced selection. The diversity pattern in Myb14 was more ambiguous but also suggested that this locus may be subjected to balancing selection. Myb4, Myb5 and Myb8 showed no or low polymorphism, which could be consistent with purifying selection. Myb2 and SCL1 did not depart from neutrality using the same tests. These contrasting results across 9 different loci were more consistent with signatures of selection than with strong demographic events, a hypothesis that also fits with the high diversity observed for neutral markers in this metapopulation. Within-gene linkage disequilibrium was found to be higher than previously described in other conifer species and did not decay with distance, except for Myb2, contrasting with most published results so far in the Pinaceae. These results underline the putative role of these transcription factors in adaptation, making them good candidates for an association mapping study.