Aim: To validate the distribution of a poultry litter-specific marker gene in faecally contaminated environmental waters of an intensive poultry litter rearing region. Methods and Results: A TaqMan â -based qPCR assay for Brevibacterium sp. LA35 16S rRNA (LA35 gene), which was previously shown to be associated with poultry litter and faeces, was tested on 126 nontarget faecal samples and 28 poultry litter and faecal samples. The TaqMan assay was sensitive (76%) and specific (100%) to the LA35 gene and exhibited a detection limit for poultry litter in water samples that is sufficiently low (2Á5 9 10 À2 mg litter l À1 ) to be applicable for environmental monitoring. The LA35 gene was detected in 43% of water samples (n = 30) collected in an intensive poultry rearing region of West Virginia which drains to the Chesapeake Bay. Conclusions: The poultry-specific TaqMan qPCR method for the LA35 gene is more specific than previously published methods and can be used to identify regions impacted by poultry rearing activities.