Background and Purpose: The aim of present research is to study intra- and inter-population genetic variation in Austrian pine by the application of biochemical markers. A better knowledge of the genetic potential of Austrian pine populations will enhance the production of seed and planting material, and in this way also the success of afforestation and the establishment of Austrian pine specific-purpose plantations. Material and Methods: The polymorphism of protein markers was determined based on the selected genotypes originating from six populations (seed stands) in Serbia. Based on the derived electrophoregrams, qualitative and quantitative differences (number and pattern) in protein fractions were identified and the seed protein profile was constructed for each tree, as well as for each of the six study populations. Analysis of protein markers was performed using two statistical methods, NTSYS and correspondence analysis. Results and Conclusion: The conservativeness of some polypeptide, i.e. the presence in all analysed genotypes is showed. On the other hand, some protein fractions were variable at the population level, and some were variable depending on the population. The degree of genetic variation among the populations was higher than the variation within the populations. There was also a high genetic variation in seed proteins within the analysed populations. Both methods (NTSYS and correspondence analysis) give the same arrangement of the analyzed populations, whereby, because of a different view of genetic distances, they can and should be combined, enabling easier and more precise understanding of mutual relationships of the observation units.