Estimating individual tree volume is one of the essential building blocks in forest growth and yield models. Ecologically based taper equations provide accurate volume predictions and allow classification by merchantable sizes, assisting in sustainable forest management. In the present study, ecoregion-based compatible volume systems for brutian pine and black pine in the three ecoregions of southern Turkey were developed. Several well-known taper functions were evaluated. A second-order continuous-time autoregressive error structure was used to correct the inherent autocorrelation in the hierarchical data, allowing the model to be applied to irregularly spaced and unbalanced data. The compatible segmented model of Fang et al. (For Sci 46:1-12, 2000) best described the experimental data. It is therefore recommended for estimating diameter at a specific height, height to a specific diameter, merchantable volume, and total volume for the three ecoregions and two species analyzed. The nonlinear extra sum of squares method indicated differences in ecoregion and tree-specific taper functions. A different taper function should therefore be used for each pine species and ecoregion in southern Turkey. Using ecoregion-specific taper equations allows making more robust estimations and, therefore, will enhance the accuracy of diameter at different heights and volume predictions.