The soils of two managed loblolly pine forests from north-central Florida were examined that have been managed with different levels of fertilization and were planted at the whole plot level with four different families of loblolly pine. We examined the proportions of carbon-containing functional groups in soil organic matter (SOM) using nuclear magnetic resonance (NMR) spectra and a terrestrial molecular mixing model to calculate the main chemical components in the density separated ‘light’ fraction (LF). The surface A horizon (0-10 cm) and the spodic horizon (one site) were examined with the organic matter components divided into carbohydrates, lignin, proteins, lipids, char, and carbony (the latter is amorphous organic matter). The carbohydrate and protein fractions for the A1 horizon ranged from 19.3-23.9% and 8.3-9.9% respectively and showed no significant difference under the fertilization intensity and family selection at either site. The contents of lignin and lipids for the A1 horizon were significantly affected by the family at one site (p<0.05), but not at the other. Notably, the lignin in the A1 horizon was closely related to the lignin of the spodic horizon (r=0.75, p<0.05) at the site where both measurements were made, suggesting that lignin is resistant to biodegradation and that it can be leached or deposited into deeper soil layers. The charcoal fraction accounted for 10.4-15.5% of LF and was significantly larger at one site than the other. In our study, the chemical composition of soil organic matter was primarily affected by the family selection treatment within a site, and across sites, the soil charcoal amounts differed. These data suggest that genetic selection may affect SOM dynamics by influencing the contents of lignin and lipids which represent stable fractions in SOM.