High frequencies of homoeologous and even non-homologous chromosome recombination in Brassica hybrids can transfer useful traits between genomes, but also destabilise synthetic allopolyploids. We produced triploid hybrids (2n = 3x = ABC) from the cross B. napus (rapeseed, 2n = 4x = AACC) × B. nigra (black mustard, 2n = 2x = BB) by embryo rescue and allohexaploid hybrids (2n = 6x = AABBCC = 54) by chromosome doubling of the triploids. These hybrids demonstrated resistance to blackleg disease (causal agent: Leptosphaeria maculans) inherited from their B. nigra parent. In order to assess the possibility of transfer of this resistance between the B genome and the A and C subgenomes of B. napus, as well as to assess the genomic stability of allohexaploids from the cross B. napus × B. nigra, frequencies of non-homologous chromosome pairing in these hybrids were assessed using classical cytogenetics and genomic in-situ hybridization. Meiosis was highly irregular, and non-homologous chromosome pairing between the B genome and the A/C genomes was common in both triploid hybrids (observed in 38% of pollen mother cells) and allohexaploid hybrids (observed in 15% of pollen mother cells). Our results suggest that introgression of blackleg resistance from the B genome into the A or C genomes should be possible, but that allohexaploids from this genome combination are likely unstable.