Forest managers need site productivity estimates for tree species growing in mixed stands. Models developed in the past are generally for pure stands and don’t factor in the effects of climate change on site productivity. Therefore, site index (SI) models were developed for black spruce (Picea mariana Mill. B.S.P.) and trembling aspen (Populus tremuloides Michx.) trees grown in natural origin mixed stands. For this, 186 trees (93 black spruce and trembling aspen each) were sampled from 31 even-aged natural mixed stands (sites) (3 trees/species/site) across Ontario, Canada. Stand height growth models were developed by incorporating climate variables during growth for each species. Stem analysis data collected from sampled trees were used to develop these models. A mixed effects modelling approach was used to fit the models. The relationship between SIs of black spruce and trembling aspen grown in mixed stands was analyzed by calculating correlation coefficients and plotting black spruce SIs against those of trembling aspen. Climate effects on site productivity were evaluated by predicting stand heights for 4 geographic areas of Ontario for the period 2021 to 2080. Three emissions scenarios reflecting different amounts of heat at the end of the century (i.e., 2.6, 4.5, and 8.5 watts m−2) were used in the stand height growth models developed here for evaluation. Climate effects were more pronounced for trembling aspen than black spruce only in the far west. The relationship between SIs of black spruce and trembling aspen trees grown in natural origin mixed stands could not be described using a linear/nonlinear mathematical function. The models developed here can be used to estimate stand height and SI of black spruce and trembling aspen trees grown in natural origin mixed stands in a changing climate. In the absence of climate data, models fitted without climate variables can be used to estimate SI of both species.