Boreal forests play an important role in the global balance of energy and CO(2). Our previous study of elaborate eddy covariance observations in a Siberian boreal larch forest, conducted both above the forest canopy and at the forest floor, revealed a significant contribution of latent heat flux (LE) from the cowberry understory to the whole ecosystem LE. Thus, in the present study, we examined what factors control the partitioning of whole ecosystem LE and CO(2) flux into the understory and overstory vegetation, using detailed leaf-level physiology (for both understory and overstory vegetation) and soil respiration property measurements as well as a multilayer soil-vegetation-atmosphere transfer (SVAT) model. The modeling results showed that the larch overstory's leaf area index (LAI) and vertical profile of leaf photosynthetic capacity were major factors determining the flux partitioning in this boreal forest ecosystem. This is unlike other forest ecosystems that tend to have dense LAI. we concluded that control of the larch overstory's LAI had a relationship with both the coexistence of the larch with the cowberry understory and with the water resources available to the total forest ecosystem. (C) 2011 Elsevier B.V. All rights reserved.