The Nothofagus genus (Nothofagaceae) in Chile includes 12 species and some hybrids among them. Some of these species are seriously threatened, presenting a low distribution and high genetic erosion. In this study a molecular marker based on seed storage proteins Nothofagus sp. was developed. Seed samples of Nothofagus alessandrii and N. glauca from two locations in southern Chile were analysed for each species. Among the different fractions of seed proteins (albumins, globulins, prolamins and glutelins) analyzed, the glutelins showed the best results, presenting conspicuous bands. Up to 39 bands were detected in both species; 22 in N. alessandrii (including 14 polymorphic) and 26 in N. glauca (21 polymorphic), with seven of them common to both species. There was a clear difference between the protein profiles of both species; we detected a preliminary value of genetic diversity in N. glauca greater than in N. alessandrii. These results, although preliminary, suggest that this marker could be useful for assessing genetic diversity in the Nothofagus genus.