The accurate evaluation of the genetic variation, both for population and evolutionary genetic studies as well as for technological improvement, constitutes a crucial point for proper conclusions and decisions. The use of molecular and biochemical genetic markers in forest tree species has become a key issue for the proper understanding of genetic variation and the resolution of practical problems. Among Nothofagus species, these markers have been used for 20 years. However, in species native to Temperate South American Forests, the first reference dates back to 10 years. This review describes the state of the art of the use of molecular markers among Nothofagus species in general with special concern in Nothofagus nervosa and N. obliqua.