This paper describes a quantitative PCR (qPCR) method for estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. The authors developed and tested nine qPCR assays to quantify the dominant groups of microorganisms in soil. The assays were designed to target specific phylogenetic groups and were tested for specificity using DNA from representative bacterial and fungal strains. The qPCR assays were further optimized using DNA from three distinct soils: a tallgrass prairie, a desert shrubland, and a coniferous forest. The results showed significant differences in microbial community structure between the three soils, particularly in the fungal/bacterial ratios. The study highlights the limitations of the method, such as potential biases in DNA extraction and the exclusion of certain microbial groups, and suggests that the qPCR approach can be adapted for more comprehensive assessments of soil microbial communities.This paper describes a quantitative PCR (qPCR) method for estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. The authors developed and tested nine qPCR assays to quantify the dominant groups of microorganisms in soil. The assays were designed to target specific phylogenetic groups and were tested for specificity using DNA from representative bacterial and fungal strains. The qPCR assays were further optimized using DNA from three distinct soils: a tallgrass prairie, a desert shrubland, and a coniferous forest. The results showed significant differences in microbial community structure between the three soils, particularly in the fungal/bacterial ratios. The study highlights the limitations of the method, such as potential biases in DNA extraction and the exclusion of certain microbial groups, and suggests that the qPCR approach can be adapted for more comprehensive assessments of soil microbial communities.