Forest ecosystems play an important role in the global carbon (C) cycle, and may help reduce atmospheric concentrations of CO₂. Forest management practices may change soil respiration rate and microbial community structure; and thereby influence C storage. This study was undertaken to understand how forest management practices affect soil respiration rates and microbial community structures and control C storage within ponderosa and lodgepole pine ecosystems in Wyoming. Four treatments (control, uneven aged, even aged and heavy harvest) in ponderosa pine and two treatments (control and managed-regeneration after clear cut) in lodgepole pine forests were selected for study. Aboveground biomass (living tree, dead wood, herbaceous and saplings) was calculated using standard allometric equations. Belowground samples (soil organic layers, soils and roots) were collected and analyzed for C using a CN Elementar Analyzer. Soils without roots were incubated under laboratory condition to compare the microbial respiration rates of different managed treatments. Microbial community structures of different stands were analyzed using the phospholipids fatty acid method. In both ecosystems control stands had higher C storage (245 Mg C/ha and 501 Mg C/ha under ponderosa and lodgepole pine, respectively) compared to managed stands with most of this C present in aboveground biomass.