Abstract: A considerable number of putative natural hybrids between G. pensilis and T. mucronatum were discovered in the National Water-Tolerant and Moisture-Tolerant Tree Species Elite Germplasm Base of Wujiang Nursery Group Co., Ltd. These hybrid plants exhibited superior growth vigor, increased resistance, enhanced tree form, and great potential for development. This study employed SSR primers derived from Glyptostrobus pensilis and Taxodium mucronatum to identify 12 putative hybrids between these two species. The results revealed that a set of 7 primers from G. pensilis, as well as 13 primers from T. mucronatum, exhibited good repeatability and specificity. By using of these selected specific primers, hybrids S1507, S1509, S1513, S1517, S1520, S1523, S1527, S201701 and S202015 were identified as hybrids between G. pensilis and T. mucronatum. Meanwhile, M1405 and M1430 were identified as pure T. mucronatum, while S1504 was determined to be a non-hybrid, not belonging to either G. pensilis or T. mucronatum. The reliable identification of the 12 putative hybrids in this study confirms the crossability between G. pensilis and T. mucronatum, establishing a theoretical foundation for their hybrid breeding. This research provides parental materials for the subsequent breeding and production of hybrids and offers stable SSR molecular markers for the identification of hybrids between G. pensilis and T. mucronatum.