The correlation of dehydrogenase isoenzyme profile with plant/tree vigour of twenty genotypes belonging to the genus Prunus and the subgenus Cerasus as well as to four commercial rootstocks (Colt, Gisela 5, Gisela 6 and MaxMa 14) was investigated in this study. Principal component analysis was applied forthe classification of the cherry rootstocks based on vigour traits and polymorphism of isoenzymes in order to determine the most usefuldehydrogenase enzyme in the preselecting process of cherry rootstocks. The most influential variables which led to the separation of low vigorous genotypes from other genotypes were isocitrate dehydrogenase, malate dehydrogenase and phosphogluconate dehydrogenase. Since both significant and negative correlations were observed between tree vigour and malate dehydrogenase, as well as between tree vigour and phosphogluconate dehydrogenase, those systems can be used for early selection of low vigour rootstocks. Our results suggest that the association between low vigour and malate dehydrogenase genotype ab provides a convenient marker that can be characterised even at the seedling stage, and could be applied in early rootstock selection and breeding programmes.