The invention discloses an Andrias davidianus female specific marker and applications thereof. The steps comprise: A, cloning and verifying a specific fragment: 1) analyzing Andrias davidianus RAD candidate female specific fragments, 2) recovering a PCR product, cloning, and sequencing, and 3) analyzing the cloned and sequenced sequence; B, identifying physiological gender through tissue slicing:1) fixing and storing a collected Andrias davidianus gonad sample, 2) carrying out step-by-step ethanol dehydration on the sample, and 3) slicing the gonad tissue, and observing and identifying the physiological gender of Andrias davidianus; C, establishing a genetic sex identification system: 1) extracting genomic DNA, 2) design specific primers, wherein a nucleotide sequence represented by the verified sequence SEQ ID NO.1 is cloned, and 3) carrying out PCR amplification according to the reaction system; and D, applying the specific molecular marker in the identification of common individuals and sex reversal individuals of Andrias davidianus. According to the present invention, the marker has advantages of simple operation, accuracy and reliability, and can identify the genetic gender of Andrias davidianus through the non-invasive sampling; and the system for identifying the gender of Andrias davidianus and the sex reversal Andrias davidianus is firstly established, the simple and easy-performing molecular biology method is provided for the genetic gender identification of Andrias davidianus, and the approach is provided for the subsequent gender control breeding of Andrias davidianus.