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Biodiversity is an essential natural resource providing raw material for evolution by natural selection. Bottleneck and founder effects lead to the lack of genetic variation and, in turn, a decreased adaptive potential and elevated risk of extinction. One of the mechanisms maintaining genetic diversity and phenotypic variation to avoid loss of heterozygosity is the acquiring of new genetic material via gene duplication. It can result from small-scale events like unequal crossing over, retroposition, or large-scale whole genome duplication (WGD). New transcriptomic patterns in polyploids lead to transcriptomic and phenotypic novelty that can facilitate increased adaptability under environmental changes. Despite the great genetic diversity potentially generated by WGD and further genome reorganization, only a few WGD events are evolutionary ‘successful.’ Macrostomum lignano, a free-living marine flatworm, is one of the astonishingly successful neopolyploid species. We uncovered the hidden polyploidy of its genome masked with intensive karyotype reorganization. The M. lignano genome consists of three subgenomes that emerged due to the formation of a large fused chromosome and its variants and maintained their heterozygosity through chromosomal rearrangements. In this study, we sought to unveil differences in gene expression and phenotypic variation among euploid and aneuploid worms of M. lignano, being hidden tetra- and hexaploids, respectively.