Knowledge of the genetic diversity of the threatened tree species in the Brazilian semiarid region may contribute to the creation of effective strategies for their preservation and future use. The aim of this study was to select ISSR (Inter-Simple Sequence Repeat) primers capable of detecting genetic polymorphism among Mimosa caesalpiniaefolia Benth. individuals for a study of the genetic diversity of this species. A total of 27 ISSR primers were tested for their ability to amplify genomic DNA of three individuals (bulk); all of them amplified regions between the simple sequence repeats of the genome, however seven ISSR primers showed a good standard of amplification compared to the others. The seven primers selected were used to amplify the genomic DNA of nine individuals and generated a total of 78 loci, of which 52.7% were polymorphic. The content of polymorphic information of the primers ranged from 0.261 to 0.489, showing that selected primers are moderately informative; bootstrap analysis determined that 51 loci were enough to estimate the genetic diversity of the samples of individuals. We concluded that the markers generated by the primers UBC 807, UBC 824, UBC 827, UBC 840, UBC 851, UBC 873 and UBC 881 allow detection of the genetic polymorphism among individuals of M. caesalpiniaefolia, being useful to determine the genetic diversity of this species.