F-statistics were employed to analyse quantitative and allozyme variation among 19 native populations of maritime pine (Pinus pinaster Ait.). Fourteen polymorphic allozyme loci were used to provide an empirical basis for constructing a null hypothesis to test natural selection as a determinant of quantitative evolution in stem form, total height growth and survival at 30 years old. Hidden biases, that may result in a difference between quantitative (Q(ST)) and allozyme (F(ST)) differentiation which are not because of the action of natural selection, were avoided by comparing pairs of populations using linear models. All quantitative traits showed higher differentiation than allozymes. The highest divergence was found in stem form, whereas divergences in total height and survival were significantly lower. Differential adaptation to regional and local patterns of precipitation, temperature and soil type seem to be the best explanation of the different structure found in quantitative traits and allozyme loci. Possible bias in the estimation of Q(ST) due to the level of quantitative within-population diversity and the role of adaptation of maritime pine after the last glaciation to highly diverse ecological conditions are discussed with special reference to the actual geographical structure of gene diversity in the species' native range.