Genomic in situ hybridization (GISH) successfully differentiated homoeologous genomes in the inter-specific hybrid Allium cepa x fistulosum, thus allowing the detection of reciprocal crossover events as label exchanges in separating anaphase I chromosomes. Three of the eight chromosome pairs were positively identified by fluorescence in situ hybridization (FISH) to rDNA sequences. There was a general similarity of the GISH-based label exchange frequencies and metaphase I chiasma frequencies, but with a 20% deficit of chiasmata. Reasons for this apparent deficit are discussed. The locations of chiasmata and label exchanges are in broad agreement.