The monilophytes Blechnum spicant (L.) Sm. and Dryopteris affinis ssp. affinis (Lowe) Fraser-Jenkins show different reproductive strategies under in vitro conditions. While B. spicant exhibits asexual and sexual reproduction, with an antheridiogen system promoting outcrossing, D. affinis ssp. affinis reproduces only asexually through apogamy. Individuals of several populations of these species, collected in Principado de Asturias (Spain), were analyzed to test the influence of their mating system in the genetic variability displayed by each species. This study shows that the genetic diversity assessed in populations of each species collected in situ is in concordance with that expected according to their reproductive system previously observed in vitro. The genetic diversity found in D. affinis ssp. affinis was low and most of genetic variation can be attributed to differences among localities. This result indicates high fixation of the detected alleles within each locality, as expected for a clonal reproductive system. In the sexual species B. spicant the genetic diversity was higher. Our results confirm the importance of reproduction system in the genetic diversity present in populations of these fern species making essential to consider the definition and study of reproductive system and the associated consequences in the design of successful conservation actions.