SummaryThe mechanisms of chromosome pairing are poorly understood. Yet, pairing during meiotic prophase is commonly assumed to indicate homology, and absence of pairing non‐homology between parental genomes. These assumptions lead to the widely accepted belief that data on chromosome pairing in hybrids provide indisputable evidence of degree of phylogenetic affinity between the parental taxa involved. Chromosome pairing usually, but not always, is a valid source of information on relationships in diploid hybrids, but rarely if ever provides conclusive evidence on affinities when polyploid taxa are involved.