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Centromeres are essential for chromosome function, yet their role in shaping genome evolution in polyploid plants remains poorly understood. Allopolyploidy, where post-hybridization genome doubling merges parental genomes that may differ markedly in chromosomal architecture, has the potential to increase centromeric complexity and influence genomic plasticity. We explore this possibility in carnivorous Caryophyllales, a morphologically and chromosomally diverse plant lineage encompassing sundews, Venus flytraps, and Nepenthes pitcher plants. Focusing on sundews (Drosera), we generated chromosome-scale assemblies of holocentric D. regia and monocentric D. capensis, which share an allohexaploid origin but have diverged dramatically in genome structure. D. regia retains ancestral chromosomal fusions, dispersed centromeric repeats, and conserved synteny, whereas D. capensis exhibits extensive chromosomal reorganization and regionally localized centromeres after a lineage-specific genome duplication. Phylogenomic evidence traces D. regia to an ancient hybridization between sundew- and Venus flytrap-like ancestors, setting it apart within its infrageneric context. Genus-wide satellite DNA repeat profiling reveals rapid turnover and species-level variation in centromere organization. Together, these results establish sundews as a natural system for investigating how centromere dynamics interact with recurrent polyploidization and episodes of ecological innovation to shape genomic resilience.