Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.

We examined the reproductive strategy of two Amazonian quillworts (Isoëtes cangae and Isoëtes serracarajensis), endemic and threatened species of canga ecosystems. Sexual propagation was examined by in vitro fertilization assays, while asexual propagation was examined by tiller emission. Isoëtes cangae is an outcrossing species that reproduces exclusively by spore germination and is able to propagate by self- and cross-fertilization. Isoëtes serracarajensis reproduces asexually by emitting tillers from the plant corm, despite producing male and female sporangia. These distinct reproductive strategies in the different species may be linked to their contrasting habitats. Isoëtes cangae inhabit a permanent oligotrophic lake with mild environmental changes, while I. serracarajensis are found in temporary ponds facing severe seasonal drought, where asexual propagation may represent an adaptive advantage to the short growth period during access to water. We also observed different relationships between plant growth and reproductive traits between the species, despite their common production of sporophytes with high survival rates. Together, these results are of paramount importance for establishing conservation plans for both species considering the advantages of sexual propagation to maintain the genetic diversity of I. cangae and the diligent management required to do the same with asexually propagated I. serracarajensis.