An assay based on the competitive polymerase chain reaction (PCR) was developed to quantify Glomus mosseae, an arbuscular mycorrhizal (AM) fungus, within plant roots. Using previously designed G. mosseae specific primers, a heterologous internal standard was constructed by amplifying Pseudomonas DNA under low stringency annealing conditions. Co-amplification of G. mosseae and internal standard DNA within leek root extracts provided accurate quantification of target DNA. Colonization of leek roots by G. mosseae was monitored in a comparative study by competitive PCR and microscopy, a conventional method of quantification. These two methods gave closely parallel data for G. mosseae colonization from three different inoculum levels over a 6 week period. Results indicate that competitive PCR is a sensitive and accurate method of quantification. The major advantage of competitive PCR over microscopy is that it can quantify specific AM fungi.