Regulation properties of biological processes are determined by their hierarchical organization in space and time. Thus the hierarchy of processes in plants covers time interval from 10^-12 s (absorption of light quanta, primary charge separation) to seconds in metabolic processes and days characteristic of the whole plant growth.

On every hierarchy level biological systems are far from termodynamical equilibrium and open for energy and matter fluxes. That is the reason why kinetic models of biological processes are nonlinear. As a result complex time-space behavior patterns together with relaxation patterns could take place, including multistable, oscillatory and quasystochastic patterns of processes.

Data of experimental research and development of mathematical models and their identification allow us to establish at least two levels of regulation in primary photosynthetic processes. Pigment-protein complexes are sensitive only to the "strong" light regulation which induces directed conformations and does not depends on pH, redox conditions and is quite similar in different species. At the diffusion-controlled stages where complexes interact with movable carriers the rate constants of reactions depend on pH, redox state and temperature. These stages are controlled by physiological state of the whole plant.

At the level of the dark processes (Calvin Cycle) oscillation patterns appear. The existence of pools of reduced substances and ATP provides possibility of autonomous CO₂ reduction, oscillations being related to the stability of the processes in wide range of external conditions. Experiments on algae show that by optimal coupling of primary and dark reactions demonstrate relaxation (non-oscillation) patterns of fluorescence induction while alteration of coupling is accompanied by complex nonmonotonous patterns with several maxima.

Time-space heterogeneity of ion concentration, electrical potential and chloroplast distribution could be observed on the Chara cell membrane, which is several cm long. Such structures are probably related with the local nonlinear systems of transmembrane ion transfer coupled to processes of photosynthesis in chloroplasts.

Thus nonlinear and hierarchical organization of photosynthetic processes provides different types of their regulation in wide range of environmental conditions.