The somaclonal variation is an event that can appear during the in vitro vegetal tissues cultures as genetic modifications in cells and tissues. This variation has been used in processes of genetic improvement and to increase the natural genetic variation. Nevertheless, when the purpose is the clonal propagation, like rubber tree micropropagation case by somatic embryogenesis, somaclonal variation is an unwanted phenomenon. This research established a methodology for somaclonal variation detection using AFLP molecular markers in Hevea brasiliensis somatic embryos of the clones IAN 710 and IAN 873 and plantlet donors of leaves for the process of somatic embryogenesis was used. This robust technique reliable allow showed variation within donating plants, and a high rate of somaclonal variation within embryogenic calluses of Hevea brasiliensis, likewise, showed high variation among embryogenic calluses and plantlet donors.