The study of the evolutionary and population genetics of quantitative traits requires the assessment of within- and among-population patterns of variation. We carried out experiments including eight Iberian Arabidopsis thaliana populations (10 individuals per population) in glasshouse and field conditions. We quantified among- and within-population variation for flowering time and for several field life-history traits. Individuals were genotyped with microsatellites, single nucleotide polymorphisms and four well-known flowering genes (FRI, FLC, CRY2 and PHYC). Phenotypic and genotypic data were used to conduct QST–FST comparisons. Life-history traits varied significantly among- and within-populations. Flowering time also showed substantial within- and among-population variation as well as significant genotype × environment interactions among the various conditions. Individuals bearing FRI truncations exhibited reduced recruitment in field conditions and differential flowering time behavior across experimental conditions, suggesting that FRI contributes to the observed significant genotype × environment interactions. Flowering time estimated in field conditions was the only trait showing significantly higher quantitative genetic differentiation than neutral genetic differentiation values. Overall, our results show that these A. thaliana populations are genetically more differentiated for flowering time than for neutral markers, suggesting that flowering time is likely to be under divergent selection.