When assigning conservation priorities in endangered species, two common management strategies seek to protect remnant populations that (i) are the most genetically divergent or (ii) possess the highest diversity at neutral genetic markers. These two approaches assume that variation in molecular markers reflects variation in ecologically important traits and ignore the possibility of local adaptation among populations that show little divergence or variation at marker loci. Using common garden experiments, we demonstrate that populations of the rare endemic plant Arabis fecunda are physiologically adapted to the local microclimate. Local adaptation occurs despite (i) the absence of divergence at almost all marker loci and (ii) very small effective population sizes, as evidenced by extremely low levels of allozyme and DNA sequence polymorphism. Our results provide empirical evidence that setting conservation priorities based exclusively on molecular marker diversity may lead to the loss of locally adapted populations.