Anchored inter-simple sequence repeats (ISSR) were used to identify 21 accessions of Jacaranda mimosifolia, collected mainly in Buenos Aires City, and the others in Mendoza, Salta and Jujuy Province and La Plata City, as part of an ornamental breeding program. DNA was extracted and purified from young leaves and amplified by four anchored primers based on dinucleotide repeats with 5′ or 3′extension. A total of 42 polymorphic bands, obtained after electrophoresis in agarose gels stained with ethidium bromide, were used to construct a molecular identification matrix. A mean of 12.75 bands per primer were generated, ranging from 140 to 1,400 bp. The genomic relationship of the genotypes was evaluated using Jaccard coefficient, and the dendrogram was constructed using UPGMA linkage method. All the accessions were differentiated by this technique, which showed a range of Resolving Power from 1.2 to 5.721. The anchored microsatellite analysis was shown to be a promising method to identify selected material in a breeding program of J. mimosifolia and with high potential to be applied to other ornamental crops.