“Red tides” are harmful algal blooms (HABs) caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humansviaconsumption of contaminated seafood. Increasingly frequent, HABs are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters. Here, we present thede novoassembled genome (~4.75 Gbp), transcriptome, proteome, and metabolome fromProrocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we studied the molecular mechanisms that underpin response to temperature stress, which is relevant to current ocean warming trends. We discovered a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. Our multi-omics analyses uncover the molecular response to heat stress in an important HAB species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation.