The cross compatibility within and between Yulania Spach and Michelia L. (Magnoliaceae) is relatively good and various such hybrids, obtained by conventional artificial hybridization, are available. The aim of the present study was to determine the extent of genome differentiation between the species involved in these crosses through the observation of chromosome pairing during meiosis in pollen mother cells (PMCs) of the hybrids. Chromosome pairing behavior was studied in five species (2n = 38) and two interspecific hybrids of Michelia, eight species (2n = 38, 76 and 114) and 10 interspecific hybrids of Yulania, and three intergeneric hybrids between Michelia and Yulania. The results showed that chromosome pairing was normal with bivalent formation in diploid parental species and in interspecific hybrids. In addition to bivalents, multivalents were encountered in polyploid parental species and polyploid interspecific hybrids. In the intergeneric hybrids between a tetraploid Yulania and two diploid Michelia, 19 chromosomes, most likely originating from Michelia, were unable to synapse from zygotene to metaphase I. Meiotic chromosome pairing indicated a high degree of homology between species within Michelia and Yulania and less homology between the genomes of these two genera. The differentiation of morphological characters and the distinctness of natural distribution also support the conclusion that these two genera are likely independent monophyletic groups. This suggests that the two genera were split at early evolution of Magnoliaceae and the overlapping characteristics in external morphology and internal structures of the two genera may be the result of parallel evolution or ancient common ancestry.