A quantitative real-time PCR assay to specifically detect and quantify the genusAlcaligenesin samples from the agricultural environment, such as vegetables and farming soils, was developed. The minimum detection sensitivity was 106 fg of pure culture DNA, corresponding to DNA extracted from two cells ofAlcaligenes faecalis. To evaluate the detection limit ofA. faecalis, serially diluted genomic DNA from this organism was mixed with DNA extracted from soil and vegetables and then a standard curve was constructed. It was found thatAlcaligenesspecies are present in the plant phytosphere at levels 102-104 times lower than those in soil. The approach presented here will be useful for tracking or quantifying species of the genusAlcaligenesin the agricultural environment.