Polyploidization is an important mechanism for introducing diversity into a population and promoting evolutionary change. It is believed that most, if not all, angiosperms have undergone whole genome duplication events in their evolutionary history, which has led to changes in genome structure, gene regulation, and chromosome maintenance. Previous studies have shown that polyploidy can coincide with meiotic abnormalities and somatic cytogenetic mosaics in Arabidopsis allotetraploids, but it is unclear whether this phenomenon can contribute to novel diversity or act as a mechanism for speciation. In this study we tested the hypothesis that mosaic aneuploidy contributes to the formation of incipient diversity in neoallopolyploids. We generated a population of synthesized Arabidopsis allohexaploids and monitored karyotypic and phenotypic variation in this population over the first seven generations. We found evidence of sibling line-specific chromosome number variations and rapidly diverging phenotypes between lines, including flowering time, leaf shape, and pollen viability. Karyotypes varied between sibling lines and between cells within the same tissues. Cytotypic variation correlates with phenotypic novelty, and, unlike in allotetraploids, remains a major genomic destabilizing factor for at least the first seven generations. While it is still unclear whether new stable aneuploid lines will arise from these populations, our data are consistent with the notion that somatic aneuploidy, especially in higher level allopolyploids, can act as an evolutionary relevant mechanism to induce rapid variation not only during the initial allopolyploidization process but also for several subsequent generations. This process may lay the genetic foundation for multiple, rather than just a single, new species. P OLYPLOIDY is a major force in shaping angiosperm evolution and plant biodiversity (Ohno 1970;Stebbins 1971;Hegarty and Hiscock 2008;Leitch and Leitch 2008;Buggs et al. 2011). Polyploids are organisms with two or more complete sets of chromosomes. Polyploidy is frequent in nature and evidence shows that most, if not all, angiosperms have undergone at least one ancient genome doubling event in their evolutionary history (Bowers et al. 2003;Blanc and Wolfe 2004;Cui et al. 2006;Soltis and Soltis 2009;Jiao et al. 2011). Two major forms of polyploidy exist: autopolyploidy, which describes multiple genomes derived from a single species, and allopolyploidy, which refers to species in which genome doubling occurred concomitantly with the hybridization of two or more species.Newly formed allopolyploids (neoallopolyploids) are subject to multiple changes from their progenitors in response to genome duplication, including structural chromosomal change, aneuploidy, genome rearrangement, epigenetic remodeling, and transcriptional change (Madlung et al. 2002;Henry et al. 2005;Huettel et al. 2008;Lim et al. 2008;Wright et al. 2009;Salmon et al. 2010;Chen 2010). Plants are generally quite plastic and can tolerate variation in the...