Many species of Ephemeroptera have been described based on either nymphs or adults. Only 10% of Ephemeroptera species in South America are known in both life stages. The current research was carried out in order to molecularly associate nymphs and adults of Ephemeroptera, using the amplified fragment length polymorphism (AFLP) technique. We obtained molecular fingerprints by the AFLP of five species: Leptohyphes albipennis, Leptohyphes coconuco, Leptohyphes ecuador, Baetodes levis and Prebaetodes sitesi. The association between nymphs and adults of L. albipennis and L. coconuco by this analysis confirmed the effectiveness of the technique. The molecular fingerprints of B. levis and P. sitesi were generated with the hope that future collections of unknown adults would match the fingerprint and solve an identification problem. We describe here for the first time the adult of L. ecuador by matching an adult trapped in the field with the DNA fingerprint of nymphs obtained by means of AFLP.