Abstract: Malus xiaojinensis Cheng et Jiang is resistant or tolerant to multiple environmental stresses, and thus a precious wild germplasm in the genus Malus Miller. Because of its apomictic reproduction character, an accurate and rapid identification of the F1 hybrid seedlings of Malus xiaojinensis is of great importance to both genetic study and utilization of the precious genes in the germplasm. RAPD (Random Amplified Polymorphic DNA) marker is a simple, fast, and economic molecular technique for identifying the hybrid of fruit trees, but the relatively low reproducibility of some bands is still a practical problem with the RAPD molecular technique. To find a solution to this problem, 79 F1 seedlings from M. xiaojinensis×M. baccata were first analyzed using RAPD molecular markers, and then the assumed hybrid seedlings based on RAPD makers were tested by using SSR (Simple Sequence Repeat) markers in this study. The results show that 72.2% hybrid seedlings identified based on RAPD markers are confirmed by SSR markers. Our results also show that two kinds of RPAD patterns, “combination of the parents’ bands” and “appearance of the non-parental band(s)”, used in combination with the number of the specific RAPD bands, can be to used to identify the F1 hybrid seedlings of M. xiaojinensis with good accuracy. As a result, our study provides new information on the utilization of RPAD markers in identification of hybrid seedlings of fruit trees.