The invention provides InDel markers for identifying purple tea tree varieties, and a combination and application of the InDel markers. The InDel markers include the InDel marker 1 and the InDel marker 2. InDel fingerprints are utilized for identifying four purple tea tree varieties including the ziyan variety, the zixian variety, the zihong variety and the zijuan variety, and 30 pairs of InDel primers are selected from whole tea tree genomes to be subjected to polymorphic screening. An identification process mainly includes the steps of: extracting total DNA of tea trees, designing the primers, conducting PCR amplification, and carrying out allele polymorphism statistics; and finally, two pairs of InDel primers (SEQ ID NO:5-8) are determined to serve as core primers for variety identification. By adopting the InDel markers, the four purple tea tree varieties can be effectively and completely distinguished, and therefore, not only can protection and popularization of the purple tea tree varieties be promoted, but also a simple, rapid, accurate and efficient identification method is provided for the four purple tea varieties which are easy to confuse on the market.