Coccolithophores have influenced the global climate for over 200million years1. These marine phytoplankton can account for 20 percent of total carbon fixation in some systems2. They form bloomsthat can occupy hundreds of thousands of square kilometres andare distinguished by their elegantly sculpted calcium carbonate exoskeletons(coccoliths), rendering themvisible fromspace3.Althoughcoccolithophores export carbon in the form of organic matter andcalcite to the sea floor, they also release CO2 in the calcificationprocess. Hence, they have a complex influence on the carbon cycle,driving either CO2 production or uptake, sequestration and exportto the deep ocean4. Here we report the first haptophyte referencegenome, from the coccolithophore Emiliania huxleyi strainCCMP1516, and sequences from 13 additional isolates. Our analysesreveal a pan genome (core genes plus genes distributed variablybetween strains) probably supported by an atypical complementof repetitive sequence in the genome. Comparisons across strainsdemonstrate thatE. huxleyi, which has long been considered a singlespecies, harbours extensive genome variability reflected in differentmetabolic repertoires. Genome variability within this speciescomplex seems to underpin its capacity both to thrive in habitatsranging from the equator to the subarctic and to form large-scaleepisodic blooms under a wide variety of environmental conditions.