It is shown that the differences in the isotopic composition of carbon in the water-soluble and water-insoluble fractions of plant leaf biomass, as well as phloem, are evolutionarily determined. They associated with metabolic reactions during assimilation and photorespiration and do not depend on the illumination mode and on the spectral ranges of headlights used in illumination. The above isotopic shifts are the cause of isotopic differences in assimilatory and photorespiratory carbon stocks that feed various metabolic processes. Due to the strict temporal and spatial organization of metabolism, carbon fluxes from the funds retain isotopic differences without complete mixing. The differences in the isotopic composition of carbon of the water-soluble fraction of biomass and carbon of phloem juice from carbon of the water-insoluble fraction are small (1–3%), but they are quite stable and easily fixed. The carbon of the water-soluble fraction is very close in isotopic composition to the carbon of the phloem and is noticeably enriched with the isotope 13C relative to the water-insoluble fraction, which makes it possible to use it as a marker in the study of assimilate transport in plants, especially during budding and fruiting. It is shown that the reason for the enrichment of autotrophic organs and tissues with isotope 12C relative to carbon of heterotrophic parts of the plant is the predominant participation in their formation of an isotopically light assimilation fund, whereas an isotopically heavy photorespiratory fund takes part in the formation of heterotrophic organs. It is shown that the manifestation of the formation of two isotopically different funds is the discovered relationship of the carbon isotope composition of leaves with their age.