Clonal forestry is a reality in the southeastern United States due to improvements in somatic embryogenesis of Pinus taeda L. Differences in below-ground carbon (C) allocation between individual genotypes could alter C sequestration and cycling in these clonal plantations. Biomass partitioning may vary between clones and in response to management practices, like fertilization. Our objective was to quantify differences in biomass partitioning due to fertilization in contrasting clones of P. taeda produced from the same full-sib cross. A two (clone)-bytwo (fertilizer)-by-four (sequential harvest) factorial randomized complete block design was replicated eight times in a greenhouse for 4 months. Trees were destructively harvested monthly following fertilizer application, so changes in biomass partitioning could be determined. Both clones responded to fertilizer with a short-term reduction in root:shoot ratio and increase in foliar biomass. These changes were ephemeral, returning to control levels within 4 months. Fertilizer responses in below-ground partitioning were due to allometric differences in one clone, but were only attributable to altered rates of development in the other. Ephemeral changes in biomass partitioning in response to fertilizer application were consistent with a theory of short-term physiological response to increased nutrient availability fueling long-term fertilizer growth responses.