A modified root exclusion method was used to separate microbial respiration from the bulk soil fraction in order to determine the effect of woody debris retention and herbicide application on microbial respiration. Respiration collars 15 cm in diameter were driven to a depth of 30 cm and 3 cm at 48 locations at two sites. The 30 cm collar was designed to sever all roots during installation and prohibit future root in-growth, providing an estimate of microbial respiration. Collars were installed in July of 2005 and monthly measurement of CO2 flux was initiated in October of 2005 with a LI-6250 infrared gas analyzer attached to a closed system dynamic respiration chamber. Mean bulk soil CO2 flux over an 11 month period was similar between sites (ca. 1.9 µmol m2 sec-1), ranging from a low of 0.4 µmol m2 sec-1 in winter to a high of 6.8 µmol m2 sec-1 during summer. Root and rhizosphere respiration (RSS) contributed on average between 6 and 40% of the total bulk soil amount during the growing season measured thus far (April – July), with herbicide treatments having lower RSS fractions than non-herbicide treatments. There was no significant difference (α = 0.1) in either soil temperature or volumetric soil moisture between collars regardless of sample period or treatment. These results indicate that this method is suitable for detecting treatment effects on microbial respiration at these sites.