Distribution of genetic variability may be correlated with life history traits, such as reproductive system, pollination. seed dispersal mode, geographical distribution, and local abundance. We used RAPD markers to study the distribution of genetic variability of six populations of Baccharis concinna (Asteraceae), a rare, dioecious and threatened shrub, endemic to Serra do Cipo, southeastern Brazil, along an altitudinal gradient, ranging from 950 to 1300 in above sea level. From 113 RAPD markers, 35 were restricted to one of the six populations. Genetic variability distribution in B. concinna populations was weakly related to the altitudinal gradient. The largest proportion of the genetic variability was due to variation within populations (82.82%, P < 0.001), while 17.18% (P < 0.001) was due to variation among populations from different elevations. Similarity among populations along the altitudinal gradient was high, ranging from 65 to 74%, suggesting an intensive gene flow among them or a recent fragmentation of an ancient population into many small populations. Dioecy and other life history traits such as wind pollination and seed dispersal may influence the distribution of the genetic variability in this species. In addition, fire and habitat fragmentation represent other important factors that influence the survivorship of this rare and threatened species, and hence the distribution of its genetic variability.