Without the natural occurrence of fire in ponderosa pine forests of the western US, lodgepole pine has started to dominate regeneration in many forest stands and may be gradually replacing ponderosa pine over time. This development, however, conflicts with recent efforts in this region to restore old-aged, open ponderosa pine forests, and active management may be needed to ensure the establishment and survival of ponderosa pine. The objectives of this study were to test the effects of various stand densities on ponderosa pine and lodgepole pine regeneration between 0.1 and 1.3 m in height, compare their seedling density, morphological characteristics, and height growth rates and determine the best morphological predictors of height growth at three sites in central Oregon. Ponderosa pine seems more persistent in forest understory conditions than lodgepole pine and a high percentage of ponderosa pine seedlings originated from advance regeneration with ages of more than 30 years commonly measured in these seedlings. Lodgepole pine seedlings, on the other hand, seemed to have established primarily after stand density reduction, as indicated by their younger minimum ages and low survival of tall seedlings, especially at high overstory densities. After stand density reduction, high rates of seedling establishment, rapid height growth and rapid crown development seem to enable this species to more quickly occupy growing space than ponderosa pine. The morphological variables best predicting absolute height growth in both species and at all three sites were absolute height growth in the previous year, the number of needle fascicles on the main stem, stem diameter at the root collar, and initial seedling height. In addition to initial seedling height and in addition to initial seedling height and overstory density, the best predictors were the number of needle fascicles on the main stem and needle density on the main stem and terminal leader. In general, there were significant effects of species, initial seedling height, and overstory density on morphological characteristics and height growth. Silvicultural treatments should consider the effects that different stand densities have on the competitive ability of ponderosa pine and lodgepole pine. Light and frequent reductions in stand density that leave significant residual canopy in these stands (>20 m2/ha), may be more favorable to ponderosa pine than to lodgepole pine regeneration. Conversely, after a higher stand density reduction more growing space is available to seedlings in the absence of serious competition with understory vegetation and may be a competitive advantage of lodgepole pine over ponderosa pine. This advantage may last into maturity and conflict with restoration efforts by inevitably changing the structure and dynamics of these ponderosa pine forests.