Background Stomatal conductance is a limiting factor of plant photosynthesis. Studies on the influencing factors of stomatal conductance amongst different species are abundant, but the effect of leaf phenotype on stomatal conductance is usually ignored in study. Here, the experiment set different intensities monochromatic blue and red light. We investigated the upper and lower epidermis stomatal traits, leaf structure, the maximum operational stomatal conductance and net photosynthetic rate of

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... oybean leaves. In addition, the contribution of leaf structure and stomatal characteristics to stomatal conductance was quantified by a new software package. Results In this study, net photosynthetic rate was tightly coupled with operational stomatal conductance, inhibited by red light and enhanced by blue light. Regardless of light environment, the maximum operational stomatal conductance was mainly affected by leaf thickness according to the analysis of contribution rate, rather than stomatal density of upper and lower epidermis. A significant positive correlation was found between leaf structure and stomatal density, but the correlation between stomatal density and stomatal size was not found. Regardless of the amounts of light intensities, stomatal density (SD), palisade tissue and specific leaf weight (SLW) were mainly regulated by blue light, whereas red light was more important to stomatal size and spongy tissue. Conclusions Although leaf thickness is more critical in affecting stomatal conductance than stomatal density, blue light mainly promotes leaf thickness and stomatal density, which coordinated each other to facilitate stomatal conductance, thereby positively regulating photosynthetic capacity.