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We quantified allozyme diversity and quantitative genetic variation within and between six populations of the locally rare Scabiosa canescens and the more common and widespread S. columbaria (Dipsacaceae). For the within-population component, we quantified allozyme diversity as the expected heterozygosity (He), followed by a sib analysis to estimate the heritability (h2) for eight vegetative and floral characters. There was no consistent association between h2 and He, or between h2 and current population size. Regarding the between-population component, we compared the overall level of population differentiation for the allozymes (FST), assumed to be selectively neutral, with the corresponding estimates for the quantitative traits (QST) to determine if the marker genes and the polygenic characters have been influenced by the same evolutionary force(s). Differences between estimates of FST and QST for S. canescens were too small to be declared as significant, indicating that neutral phenotypic evolution has led to the observed differentiation in this species. Our data indicate higher levels of phenotypic differentiation in S. columbaria with values of QST exceeding the allozymic FST for all traits. This finding indicates a great potential for S. columbaria to respond to local selection pressures, perhaps explaining why this species has a broader ecological amplitude than S. canescens. [ABSTRACT FROM AUTHOR]