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Author summary This study assesses the interplay between the globally distributed microalga Emiliania huxleyi and its specific lytic viruses, EhV, which drive the termination of vast oceanic blooms. E. huxleyi is characterized by a biphasic life cycle that alternates between morphologically dissimilar diploid and haploid cells. Here, we show that during viral infection, the bloom-forming diploid cells that are sensitive to EhV can produce virus-resistant cells. These latter cells are morphologically similar to the haploid phase but have diploid or aneuploid genomes. Therefore, a mechanism that mediates morphological remodeling appears to be activated during viral infection, enabling E. huxleyi to escape EhV. These results provide novel insights into morphological plasticity and viral resistance in marine phytoplankton, while highlighting the complexity of host–virus interactions in the oceanic microbial realm.