Feces from avian make a significant contribution to the contamination of water and soil environment and increase the human health risk due to the presence of various pathogens. Therefore, it is important to identify accurately and control efficiently the sources of fecal pollution for environmental protection and human health. Microbial source tracking (MST) technique based on molecular markers could identify the sources of fecal contamination from human or animals, which is helpful to distinguish and control the sources of fecal pollution in time. Due to the adverse effects of avian feces on the environment as well as human health, much more attention has been paid to develop the MST markers and applied to trace the avian fecal pollution. In this review, the sensitivity and specificity of molecular markers targeting avian such as chicken, duck, pigeon, seagull, Canada goose and sandhill crane were summarized. The gene sources for avian molecular markers, including bacterial 16S rRNA gene, mitochondrial DNA (mtDNA) and functional genes, were emphatically reviewed. Among them, bacterial 16S rRNA gene was widely used to design MST markers for avian, and the source indicators mainly included Firmicutes, Bacteroidales, Actinobacteria, Proteobacteria, and Fusobacteria. However, mtDNA, such as cytb gene, ND5 gene, 16S rRNA gene and ND2 gene, exhibited the best performance characteristics and was considered as a promising tool to detect fecal contamination from avian. Interestingly, the avian MST markers developed from functional genes showed low sensitivity, but the idea of using functional genes to design MST markers was worthy of reference. The capability of avian MST markers to distinguish fecal contamination was analyzed and compared, which provided theoretical support for researchers with the rapid selection of poultry markers. In addition, the existing problems of MST technology in avian were also analyzed and summarized, and its development in China was prospected, aiming at providing a reference for the development and application of MST technology in the monitoring of environmental quality in China.