On the example of male and female shoots of young (140 year), mature (235 year) and old (346 year) Siberian stone pine trees from southeast of West Siberia (between Ketj and Chulym rivers) influence of tree age on correlation between vegetative and generative morphogenesis was analyzed. It is shown that significance of features characterizing vegetative development of female shoots declined linearly trough reproductive period of ontogenesis. The features of generative development and indirectly related vegetative features change parabolic with maximum value in mature trees. The structure of male shoot change similarly. In the middle part of reproductive period the direct and indirect relationships between vegetative and generative features increase. The more intensive vegetative shoot organogenesis of young trees leads to minimization of cone initiation. In mature trees decreasing of vegetative development influence positively on cone formation. The maintenance of such tendency through aging even increases relationships between vegetative and generative features. It was hypothesized that discussed age-specific differences in shoot morphogenesis depends on (1) changing of correlation between vegetative and generative organogenesis during seasonal cycle of shoot development and (2) changing through ontogenesis of functional correlation between roots and crown.