ABSTRACT The jaboticaba tree (Plinia sp.) is a native fruit tree belonging to the Myrtaceae family, which occurs spontaneously throughout Brazil. The estimation of genetic divergence among genotypes of native populations can be useful for conservation and knowledge of available genetic resources, in the formation of gene banks and breeding species. In order to evaluate the genetic diversity of jaboticaba trees identified in the Bahia Reconcavo municipalities, 35 genotypes were characterized by ISSR primers (Inter Simple Sequence Repeats). The 18 primers generated a total of 463 amplicons, and the number of initiator fragments ranged from 14 to 36, with an average of 25.72% and 99.65% polymorphism. Polymorphic information content ranged from 0.13 to 0.33 with a mean of 0.22 and the marker resolution power from 4.34 to 15.77, with an average of 8.67. Multivariate analysis allowed the formation of five groups of genetic divergence, where the longest distance was 0.97 between JCA6 and JSF8 genotypes and the lower of JMT2 and JCA1 (0.11). From the use of ISSR markers it is possible to check the variability between genotypes on the evaluated jaboticaba trees.