【Objective】Early identification and selection of parents of mango seedlings by ISSR molecular markers were conducted to provide references for improving mango breeding efficiency based on ISSR molecular markers. 【Method】Using ISSR marker technology，different primers were screened to identify male parent of 97-1 seedling. 【Result】According to the optimized ISSR reaction system， four specific primers were chosen from 18 primers（UBC-848， UBC-857，UBC-864 and UBC-868）， which had many amplified bands， strong stability， high polymorphism and clear backgrounds. Jyhua mango， Sichuan red-skin mango and 97-1 seedlings were amplified using primers UBC-846，UBC-857，UBC-864 and UBC-868. The length of the amplified fragments was 100-2000 bp. The size of specific bands of Sichuan red-skin mango， Jyhua mango and 97-1 seedlings was 180 and 380 bp， 280 and 380 bp， 180 and 680 bp， and 680 and 770 bp. 【Conclusion】Through the identification system construction of mango seedling parents using ISSR molecular markers and primers UBC-846，UBC-857，UBC-864 and UBC-868， it was conclude that the male parent of 97-1 seedlings was Sichuan red-skin mango and 97-1 seedlings were the crosses between Jyhua mango and Sichuan red-skin mango.