Within the tropical flowers, heliconias are remarkable for their diversity in shape, color, size and durability especially. These features give the family Heliconiaceae great potential in the ornamental market, and in this case, floriculture, as growing economic activity requires the use of techniques and strategies that allow for efficient troubleshooting. Within the current promising strategies to reach the requirements of quantity, quality and fidelity of the flowers is in vitro culture, but one of its problems is the appearance of somaclonal variation and disadvantages related to identification of material. The aim of this study was to characterize with molecular markers AFLP genotypes of Heliconia caribaea and H. orthotricha propagated in vitro and evaluate the genetic stability of H. caribaea seedlings, it was necessary to compare the banding pattern obtained with the AFLP, to confirm and defining species plants and analyze the usefulness of AFLP markers for estimating genetic similarity and stability of heliconia plants. The results showed that with using 3 pairs of combinations AFLP was possible to differentiate the genotypes studied and make a genetic approach to species level, which grouped with genotypes of H. caribaea and H. orthotricha respectively. It is also possible to suggest the presence of somaclonal variation within clones of H. caribaea evaluated, which may have been influenced by factors such as type of explant used, hormone concentration and the number of subcultures made. However, the analysis by this technique did not discriminate specific cultivars of H. orthotricha and H. caribaea because of the high intra -and inter- variability of these genotypes and also the AFLP technique is not ideal for evaluating this objective because when individuals have such genetic variability.