A suitable marker for microbial source tracking (MST) remains difficult to find in China due to the geographical variability of markers. 162 faecal and litter samples were collected from five different regions in China to identify the faecal pollution from poultry with nine published molecular markers for MST. All samples tested were positive for both universal markers BacUni and MI50, but BacUni was detected with higher gene copies. Of the avian-associated AV4143 and GFD assays, the AV4143 was modified here with the accuracy of 88% which proved its potential in identifying faecal pollution from avian. For all poultry-associated markers tested, the best performance characteristics were shown in marker Ckmito (accuracy of 97%), followed by ND5-CD (accuracy of 88%), and finally LA35 and Chicken-Bac (accuracy of ≤ 77%). A combination of mitochondrial DNA (mtDNA) markers Ckmito and ND5-CD is recommended to differentiate the contamination caused by poultry. LA35 was more sensitive in poultry litter (100%) than in poultry faeces (21%). Our findings regarded BacUni, AV4143, and a combination of Ckmito and ND5-CD as the best performing universal, avian, and poultry assays, respectively. Suitable molecular markers could assist with efforts to determine the faecal pollution sources in environmental monitoring.