The effects of intensive plantation management and genetics on soil carbon cycling are poorly understood. The soil carbon fractionation schemes also need to be optimized based on soil types and study questions. This study was undertaken with the following objectives: 1) to examine the effects of family and family x management interactions on soil carbon in a forested Spodosol; and 2) to evaluate the distribution of soil carbon across different size-density fractions and to identify the most responsive carbon pools in these soils. A replicated factorial experiment, consisting of two levels of management (fertilization and chemical weed control), two planting densities and six full-sib families, was established in north Florida. At age 6 yr, replicated surface soil samples were collected from three families (best, medium and poor; designated a priori based on growth) and both levels of management intensity from the high planting density plots. Dry sieving and a modified density fractionation procedure were used to separate the carbon pools, while a modified sonication procedure was used to measure aggregate carbon. These procedures proved sensitive enough to detect genotype and management effects in as few as four years. The best family tended to have more decomposable organic matter as shown by 59% higher carbon in the light density. The medium family was associated with higher aggregation (9-17 %) in the medium and heavy density fractions. The medium family also exhibited 34% higher N content in the medium density fraction than the best family under the low intensity management. The medium density 2000 to 250 μm fraction contained the most C, while the heavy density 250 to 150 μm fraction contained the most N. These results suggest the potential of using genetic deployment for improved carbon sequestration and indicate the need to understand long-term effects of genetics on soil carbon pools.