The 10 ISSR primers identified in the first stage of this study amplified 221 loci when evaluated in the seven populations of A. flaccida. Of these, 190 (85.97%) were polymorphic in all populations. The degree of polymorphism did not show a high variation among populations, with the lowest and highest values of 55.2% and 63.8% in the Porto Barreiro and Campos Novos populations, respectively.