|Faecal pollution on bathing beaches poses a potential threat to human health and as a result may also negatively affect the local economy. In instances where the source of such pollution is not obvious, it may be necessary to track such sources using a host-specific genetic markers technique. Bacteroides species are potential indicators for source tracking of faecal pollution in bathing waters. This study designed specific primer sets to amplify sections of the 16S rRNA gene unique to Bacteroides from domestic dogs and used quantitative PCR (qPCR) to quantify such genetic markers in environmental samples. The sensitivity and specificity of the primer sets was determined; they were specific in silico against known dog Bacteroides sequences and in vitro against Bacteroides sequences originating from human and livestock faeces. Dog faecal Bacteroides contamination was then detected in sea water during the bathing season at a local beach where dogs are banned during the summer months, in spite of the fact that these waters had met EU directive standards based on the culture-based enumeration of faecal indicator bacteria. Quantitative PCR was used to determine the limit of detection (LOD) of the dog Bacteroides genetic markers in these water samples. The copy number of dog Bacteroides genetic markers in the water was low and the LOD of those markers was 4 copies per reaction. The use of these dog primers has the potential to supply important additional information when source tracking faecal pollution at bathing beaches and maintaining water quality. Hussein KR, Waines PL, Nisr RB, Glegg G, Bradley G (2014) Development and use of Bacteroides 16S rRNA Polymerase Chain Reaction Assay for Source Tracking Dog Faecal Pollution in Bathing Waters. Hydrol Current Res 5:163. doi: 10.4172/2157-7587.1000163.