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Polyploidy (whole genome duplication) is a major contributor to eukaryote genome evolution but newly formed polyploids face many hurdles becoming established. A major challenge is correctly segregating multiple related chromosome sets during meiosis, with segregation errors often leading to reduced fertility. This is exemplified in the model allopolyploid species Arabidopsis suecica, with first generation “synthetic” polyploids having an abnormal meiosis and low fertility, while established natural populations have evolved a stable meiosis and are highly fertile. We have characterised the meiotic behaviour of evolved and synthetic A. suecica and observe that the loss of fertility in synthetic lines is associated with major meiotic abnormalities including asynapsis and illegitimate recombination. We are now using forward and reverse genetics to investigate the pathways which underlie these differences in meiotic behaviour. These, and future, insights into the determinants of meiotic recombination stringency will further our understanding of polyploid formation as well as the barriers to gene-flow in both wild populations and (pre-)breeding programmes.