Changes in structure and physiological features of different ecotypes of the Siberian stone pine (Pinus sibirica Du Tour.) growing in common climate conditions in the south of Tomsk Region are discussed. The grafts of mother trees taken from natural northern, western and eastern marginal populations have been investigated. It is shown that northern ecotypes have smaller size needles, smaller areas of cross section, mesophyll, and conducting bundle, lower green and yellow pigment content as well as decreased functional activity of chloroplasts in comparison with local variants. In the longitudinal direction, differences between the ecotypes are less pronounced, however the local ecotype has higher values of the parameters controlled.