A carbon- and nitrogen-balance model, applying pipe model theory and a modification of functional balance as growth-guiding rules, is presented for the grass stage pine seedlings. Three populations of Pinus merkusii Jungh. et de Vriese, originating from northern and northeastern Thailand, were grown under controlled environment for 47 weeks to obtain parameter information, to evaluate the model performance and to investigate genotypic variation in various characteristics among the populations. Monte Carlo simulations were used to evaluate the sensitivity of the model behaviour to varying parameter values and to calibrate the model for each population. With given sets of parameter values, the simulated biomass development fitted rather well the observed one during the experiment. The two most important parameters determining model performance were within-shoot shading and specific nitrogen uptake rate of fine roots. The fit of simulated versus measured fine roots had a major effect on acceptable model performance in Monte Carlo simulations. Significant variation in biomass growth, nitrogen use efficiency, height, stem diameter, total carbon concentrations of stem and fine roots, and total nitrogen concentrations of needles, transport roots and fine roots was found among the populations. The observed genotypic variation in seedling biomass and stem diameter was consistent with the geographical distribution of the populations while the variation in the rest of the measured characteristics was not. It seems that P. merkusii populations in Thailand are adapted to more site specific conditions rather than climatic conditions alone, and that the variation in biomass growth may result from variation in internal carbon and nitrogen dynamics among the populations.