ABSTRACT Sodom apple is a plant species adapted to various ecosystems and has stood out for its economic and ecological importance. We evaluated the amplification profile of 23 ISSR primers and selected polymorphic loci for genetic studies of a natural population of Calotropis procera by collecting and extracting genomic DNA from 33 individuals. Genomic DNA was extracted using the sorbitol protocol and 2% CTAB and the ISSR amplification products were resolved by electrophoresis. Based on the amplification profile, the 23 primers were classified as suitable, moderate, and unsuitable. We described the quality of primers considering the total number of bands, mean bands per primer, percentage of polymorphism, Nei’s genetic diversity (expected heterozygosity – He), assuming Hardy-Weinberg equilibrium and the polymorphic information content (PIC). All ISSR primers showed an amplification profile, which generated 173 bands with an average of 7.5 loci per primer. However, only 18 out of the 23 tested primers allowed visible and high-quality amplification, which were classified as suitable and polymorphic. We also observed a mean of 0.30 and 0.24 for PIC and He estimates, respectively. The DiCA3`RG, TriAGA3`RC, and TriCGC3`RC primers were highly transferable to C. procera (they presented quality for amplification with good reproducibility), with PIC values higher than 0.40, He higher than 0.30, and polymorphism higher than 86%.