Genetic engineering has been used to decrease the lignin content and to change the lignin composition of switchgrass (<
italic>
Panicum virgatum<
/italic>
L.) to decrease cell wall recalcitrance to enable more efficient cellulosic biofuel production. Previous greenhouse and field studies showed that downregulation of the gene encoding switchgrass caffeic acid<
italic>
O<
/italic>
-methyltransferase (COMT) and overexpression of the switchgrass<
italic>
PvMYB4<
/italic>
(MYB4) gene effectively improved ethanol yield. To understand potential environmental impacts of cultivating these transgenic bioenergy crops in the field, we quantified the effects of field cultivation of transgenic switchgrass on soil organic carbon (SOC) dynamics. Total and active SOC as well as soil respiration were measured in soils grown with two COMT-downregulated transgenic lines (COMT2 and COMT3), three MYB4-overexpressed transgenic lines (L1, L6, and L8), and their corresponding non-transgenic controls. No differences in total SOC, dissolved organic carbon (DOC), and permanganate oxidizable carbon (POXC) were detected between transgenic and non-transgenic treatments for both COMT (10.4?11.1 g kg<
sup>
-1<
/sup>
for SOC, 60.0?64.8 mg kg<
sup>
-1<
/sup>
for DOC, and 299?384 mg kg<
sup>
-1<
/sup>
for POXC) and MYB4 lines (6.89?8.21 g kg<
sup>
-1<
/sup>
for SOC, 56.0?61.1 mg kg<
sup>
-1<
/sup>
for DOC, and 177?199 mg kg<
sup>
-1<
/sup>
for POXC). Soil CO<
sub>
2<
/sub>
-carbon (CO<
sub>
2<
/sub>
-C) production from the COMT2 transgenic line was not significantly different from its non-transgenic control. In contrast, the COMT3 transgenic line had greater soil CO<
sub>
2<
/sub>
-C production than its non-transgenic control (210 vs. 165 �g g<
sup>
-1<
/sup>
) after 72 days of laboratory incubation. Combining the improvement in ethanol yield and biomass production reported in previous studies with negligible change in SOC and soil respiration, COMT2 could be a better biofuel feedstock than COMT3 for environmental conservation and cost-effective biofuel production. On the other hand, MYB4 transgenic line L8 produced more biomass and total ethanol per hectare while it released more CO<
sub>
2<
/sub>
-C than the control (253 vs. 207 �g g<
sup>
-1<
/sup>
). Long-term in situ monitoring of transgenic switchgrass systems using a suite of soil and environmental variables is needed to determine the sustainability of growing genetically modified bioenergy crops.