We measured the ?13C of assimilated carbon (foliage organic matter (?COM), soluble carbohydrates (?CSC), and waxes (?CW)) and respiratory carbon (foliage (?CFR), soil (?CSR) and ecosystem 13CO2 (?CER)) for two years at adjacent ecosystems in the southeastern U.S.: a regenerated 32 m tall mature Pinus palustris forest, and a mid-rotation 13 m tall Pinus elliottii stand. Carbon pools and foliage respiration in P. palustris were isotopically enriched by 2‰ relative to P. elliottii. Despite this enrichment, mean ?CER values of the two sites were nearly identical. No temporal trends were apparent in ?CSC, ?CFR, ?CSR and ?CER. In contrast, ?COM and ?CW at both sites declined by approximately 2‰ over the study. This appears to reflect the adjustment in the ?13C of carbon storage reserves used for biosynthesis as the trees recovered from a severe drought prior to our study. Unexpectedly, the rate of ?13C decrease in the secondary C32–36 n-alkanoic acid wax molecular cluster was twice that observed for ?COM and the predominant C22–26 compound cluster, and provides new evidence for parallel but separate wax chain elongation systems utilizing different carbon precursor pools in these species. ?CFR and ?CER were consistently enriched relative to assimilated carbon but, in contrast to previous studies, showed limited variations in response to changes in vapor pressure deficit (D). This limited variability in respiratory fluxes and ?CSC may be due to the shallow water table as well as the deep taproots of pines, which limit fluctuations in photosynthetic discrimination arising from changes in D.