The specificity of a short fragment functional gene marker (alpha-1-6, mannanase) in Bacteroides thetaiotaomicron was compared with two other Bacteroidales markers used for identifying sewage as the source of pollution in water. A total of 11 different animal species and 230 faecal samples were tested using quantitative polymerase chain reaction. The results showed that the alpha-1-6, mannanase marker had high specificity (0·97). Limited cross-reactivity was found in swine, gull and cat faeces with copy numbers close to detection limit. Positives were detected in all bovine and sheep faeces tested for the Human-Bac1 marker. The human-specific alpha-1-6, mannanase marker showed greater specificity (0·97) than the HF 183 Bacteroides PCR marker (0·71) and the Human-Bac1 (qPCR) marker.