This study was aimed to investigate the stability of chromosomes during meiosis in autopolyploid and allopolyploid maize, as well as to determine an association of chromosomes between maize (Zeamaysssp.mays Linnaeus, 1753) andZ.perennis(Hitchcock, 1922) Reeves & Mangelsdor, 1942, by producing a series of autopolyploid and allopolyploid maize hybrids. The intra-genomic and inter-genomic meiotic pairings in these polyploids were quantified and compared using dual-color genomic in-situ hybridization. The results demonstrated higher level of chromosome stability in allopolyploid maize during meiosis as compared to autopolyploid maize. In addition, the meiotic behavior ofZ.perenniswas relatively more stable as compared to the allopolyploid maize. Moreover, ten chromosomes of "A” subgenome in maize were homologous to twenty chromosomes ofZ.perennisgenome with a higher pairing frequency and little evolutionary differentiation. At the same time, little evolutionary differentiation has been shown by chromosomes of "A” subgenome in maize, while chromosomes of "B” subgenome, had a lower pairing frequency and higher evolutionary differentiation. Furthermore, 5IM+ 5IIPP+ 5IIIMPPand 5IIMM+ 5IIPP+ 5IVMMPPwere observed in allotriploids and allotetraploids respectively, whereas homoeologous chromosomes were found between the "A” and "B” genome of maize andZ.perennis.