Six Nierembergia linariaefolia clones were selected for ornamental traits during a native germplasm development program. For fingerprinting diagnosis, 13 anchored inter-simple sequence repeat (ISSR) primers and 6 amplified fragment length polymorphism (AFLP) primer-enzyme combinations were used. Both markers revealed high levels of polymorphism, enabling genetic discrimination of the accessions analyzed by using 443 informative ISSRs and 541 AFLP markers. Both molecular techniques are suitable for monitoring genetic diversity in Nierembergia linariaefolia and, under our experimental conditions, they showed correlation coefficients of 0.629 for similarity matrices and of 0.649 in the cophenetic matrices. These results suggest that ISSRs are a good choice for DNA analysis in N. linariaefolia when simple manipulation and a low budget are required.