Carbonate accumulation in the deep-sea is largely sustained by pelagic carbonate producers, in the form of calcite platelets (coccoliths) produced by calcifying haptophyte algae and the calcite tests of planktic foraminifera. But pelagic producers have not always dominated the carbonate production during the Phanerozoic. The first part of the Phanerozoic is also known as the "Neritan ocean" where the carbonate production was supported by benthic producers in carbonate platforms. The second part of the Phanerozoic is known as the "Cretan ocean" where the carbonate production was supported by pelagic producers. The transition from benthic to pelagic was a revolution in carbonate production, deeply changing the organization of the carbonate system in the oceans. This revolution is named the Kuenen Event. This transition was initiated by the development of pelagic producers during the Mesozoic. This study discusses the timing of the Kuenen Event and the role of the evolution of coccolithophores. We have compiled quantitative data of the absolute abundance and burial fluxes of coccoliths in the sedimentary record over the past 200 Ma. Burial fluxes increased from the Early Jurassic reaching a maximum during the Early Cretaceous. Then, the record fluctuates in average but maximum values remained the same for the rest of the Mesozoic. Meanwhile, coccolith species diversity increased from the Early Jurassic until the K/Pg crisis. During the Cenozoic, species diversity increased until the Early Eocene and subsequently decreased. Flux and diversity have different patterns and we propose a model of coccolithophore evolution in two steps during the Mesozoic with 1) until the Early Cretaceous (~135 Ma), the invasion of the environments and 2) until the K/Pg crisis (~66 Ma) the specialization of coccoliths leading to the compartmentalization of ecological niches. No model is yet proposed for the Cenozoic until we have more data. Finally, although coccolithophores seem to have reached a maximum in production in the Early Jurassic, there are no clear and recurrent observations of coccolith-formed or pelagic carbonate deposits until the Late Cretaceous. Therefore we hypothesize that the Kuenen Event was a long-term event during the Mesozoic which likely started with the appearance of coccolithophores and ended with the diversification of planktic foraminifera.