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The investigation of hybridization processes and embryogenesis of heterozygote is an effective approach for early hybrids’ identification, which could provide reliable information for successful crossbreeding. In this study, we reported the whole hybridization processes of the direct cross and reciprocal cross between Michelia yunnanensis Franch. ex Finet et Gagnep. and Michelia crassipes Law using fluorescence microscopy after aniline blue staining, with the pollen germination on stigmas, pollen tube growth in styles, and subsequent extension into the embryo sac as well as the double fertilization processes are documented in detail. The M. yunnanensis × M. crassipes combination displayed considerable cross-compatibility, and the heterozygote embryogenesis was further observed with an approach of modified cryosectioning technique. Besides, the whole formation processes of hybrid seeds from artificial pollination to maturation were successfully observed. However, in the reciprocal cross, we found incompatibility between pollen grains of M. yunnanensis and stigmas of M. crassipes for the reason of hysteretic identification, as well as the abnormal callose deposition which belongs to the prefertilization barriers. This is the first study in which the complete and clear hybridization processes in Michelia were reported. We inferred that unilateral incompatibility of M. crassipes detected in this study may also exist in some other Michelia species. In artificial hybridization practices, we suggest some special treatments for overcoming prefertilization barrier should be taken when treating M. crassipes as the maternal parent.