Background and aims: DNA-based methods present new opportunities for overcoming the difficulties of accurately identifying and quantifying roots of different plant species in field soils. In order to quantify species-specific root biomass from measurements of DNA, consideration needs to be given to replication and ability to recover roots for calibration purposes in order to account for spatial, temporal and inter- and intra-species variation in DNA content of roots and distribution of roots within the soil profile. Methods: This paper develops the field application of a DNA-based technique for direct quantification of roots in soils. The method was applied to a field experiment to investigate differences in root growth of acid-soil resistant and sensitive genotypes of perennial pasture grasses in an acid soil. DNA was extracted directly from soil and species-specific DNA was quantified using quantitative real-time PCR prior to estimation of root biomass. Results: Root growth of the perennial grasses was quantified using the DNA-based technique, although separate calibration procedures were needed to convert DNA content to root mass for each species, soil layer and sampling date. Compared to acid-soil resistant genotypes, lesser root growth in acid soil layers and reduced above-ground dry matter production was observed for acid-soil sensitive genotypes. Conclusions: The DNA-based method allowed genotypic differences in root growth to be assessed directly in soil and was advantageous for rapid processing of a large number of samples. However, high replication was still required to overcome spatial variability and separate calibrations were required for different species and soil depths across sampling times. The technique demonstrated greater root growth of acid-soil resistant perennial grasses which was beneficial for their establishment and persistence.