The relationship between heretozygosity and vegetative fitness was explored in the narrow endemic and threatened Clematis acerifolia (Ranunculaceae), both at individual and population levels. The relationships between fitness, habitat factors, and population size were also analyzed. Allozyme electrophoresis was used to quantify the levels of heterozygosity of nearly 200 surveyed individuals belonging to the nine extant populations of this species. Six parameters of vegetative fitness were measured: plant height, shrub diameter, length of the largest leaf, width of the largest leaf, mean number of leaves/stem, and total number of stems. The percentage of tree cover (light availability) was measured as an indicator of habitat quality. A principal component analysis reduced the original fitness variables to two uncorrelated principal components. None of these correlated significantly with both heterozygosity and population size, in contrast to the expected result. Nevertheless, one of the principal components showed a positive relationship with light availability, which may indicate that habitat quality may have significant effects on the performance of this species. Thus, to ensure the viability of this endangered species, maintenance of adequate habitat quality (by avoiding further fragmentation) may be more important than maximizing genetic diversity within populations.