It is a long-standing debate in evolutionary biology whether natural selection can generate divergence in the face of gene flow. Comparative studies of quantitative genetic and neutral marker differentiation have provided means for detecting the action of selection and random genetic drift in natural populations. We estimated the degree of population divergence in several quantitative traits and compared these estimates with that based on presumably neutral molecular markers (random amplified polymorphic DNA [RAPD]). This approach allowed us to disentangle the effects of divergent selection from that of other evolutionary forces. Nine populations of Cakile maritima, which encompasses the complete range of distribution of this species in Tunisia, were examined. We found a high proportion of total genetic variance to be among populations and among ecoregions for quantitative traits (range of QST: 0.44-0.88) and a moderate one for RAPD markers (GST: 0.081). In addition, almost all characters displayed a significant higher QST than GST, indicating occurrence of phenotypic plasticity and local adaptation. The latter is explicable as there is no reason to expect that natural selection would affect in similar fashion all traits and affect all populations at a similar level. We also found a negative and significant correlation between genetic variation in molecular marker loci and quantitative traits at the multitrait scale. This result attests that the evolution of these markers in C. maritima were not paralleled, suggesting that the degree of genetic differentiation in neutral marker loci is closely predictive of the degree of differentiation in loci coding quantitative traits and the majority of these neutral markers negatively controlled the studied quantitative traits.