In this study we have analysed and compared the genomic composition, meiotic behaviour, and meiotic affinities of Zea perennis and Zea mays ssp. mays. To do so we studied the parental taxa and the interspecific hybrid Zea perennis x Zea mays ssp. mays, using classical cytogenetic methods, as well as GISH and FISH. GISH enabled us to recognize the genomic source of each chromosome involved in the meiotic configurations of this hybrid, and established the genomic affinities between their parental species. The results obtained here reinforce the hypothesis of the amphiploid origin of Zea perennis and, together with previous research, indicate that the chromosomes with divergent repetitive sequences in maize and Zea luxurians could be the remnants of a relict parental genome not shared with Zea perennis.