The genetic diversity of Myrciaria floribunda, a common Atlantic Forest tree, was investigated in six populations located in two small fragments (10 and 18 ha), two medium-sized fragments (36 and 44 ha) and one large fragment (3003 ha). Two populations occur in the large fragment. It is expected that smaller fragments should have lower genetic diversity and higher inbreeding. Distances between fragments varied from 0.66 to 10 km. On average 32 young trees smaller than 20 cm basal girth were sampled in each population. Allozyme electrophoresis was carried out, and six loci were scored. The effective number of alleles was lower for populations of the two small fragments (1.46 and 1.51) and higher for populations of the large (1.62 and 1.71) and medium ones (1.69 and 1.84). Small fragments showed lower values of expected and observed heterozygosities than large and medium fragments. Most of the genetic variability occurs within populations, and there was a moderate genetic variation among them ($\hat{\theta}_p$ = 0.097). Our findings show a tendency of lower genetic diversity within small and isolated fragments and higher genetic differentiation among them. But, few correlations between genetic diversity indices and fragment features (size and isolation) were significant.