Negative effects of small population size on fitness, so-called Allee effects, may threaten population persistence even in intact habitat remnants. We studied genotypes of 14 isolated populations of the clonal plant Ranunculus reptans, for which molecular genetic (RAPD-) variability is higher for large than for small populations. In a competition-free greenhouse environment vegetative offspring of genotypes from large populations produced more rosettes and flowers, indicating higher fitness. Within-genotype coefficients of variation in performance traits, indicating developmental instability, were lower for genotypes from populations with higher RAPD-variability. In competition with a taller grass, we found relative reduction in leaf length less pronounced for plants from large populations, suggesting higher adaptive plasticity. Our experimental study of a plant with predominantly vegetative reproduction suggests, that negative genetic effects of recent habitat fragmentation, which so far rather were expected in plants with frequent sexual reproduction, are more severe and more common than previously acknowledged.