Members of the genus Quercus exhibit semi-determinate growth, resulting in complex and developmentally variable endogenous physiological patterns. The Quercus morphological index (QMI; Hanson et al. Tree Physiol. 2:273-281, 1986) was developed as a tool to relate physiological patterns to morphologically identifiable ontological stages, thereby allowing for treatment or measurement of seedlings at uniform ontological stages rather than strictly by chronology. Although clear physiological patterns relative to seedling ontogeny have been observed using the QMI in pre-transplant half-sibling seedlings, we sought to determine whether physiological patterns remain consistent across genotypes within a species. We examined net photosynthesis, transpiration, leaf chlorophyll concentrations, and chlorophyll fluorescence (Fv/Fm) throughout the first flush after transplant for northern red oak (Quercus rubra L.) seedlings from three half-sibling families. Neither net photosynthesis nor transpiration rates varied by family, whereas leaf chlorophyll concentrations and Fv/Fm differed significantly. Despite family differences for magnitudes of some parameters, no interactions between QMI growth stage and family were observed, and patterns of all parameters relative to growth stage were consistent across families. Net photosynthetic rates, transpiration rates, and Fv/Fm increased during the flush, while leaf chlorophyll concentration decreased, suggesting that chlorophyll synthesis is not a limiting factor during leaf maturation in this species. Findings indicate that QMI-based physiological patterns may be at least regionally applicable within a given Quercus species.