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<p>The rise of calcareous nannoplankton in Mesozoic oceans has deeply impacted ocean chemistry and contributed to shaping modern oceans. Nevertheless, the calcareous nannoplankton colonization of past marine environments remains poorly understood. Based on an extensive compilation of published and unpublished data, we show that their accumulation rates in sediments increased from the Early Jurassic (<span class="inline-formula">∼200</span>&thinsp;Ma) to the Early Cretaceous (<span class="inline-formula">∼120</span>&thinsp;Ma), although these algae diversified up to the end of the Mesozoic (66&thinsp;Ma). After the middle Eocene (<span class="inline-formula">∼45</span>&thinsp;Ma), a decoupling occurred between accumulation rates, diversity and coccolith size. The time series analyzed points toward a three-phase evolutionary dynamic. An invasion phase of the open-ocean realms was followed by a specialization phase occurring along with taxonomic diversification, ended by an establishment phase where a few small-sized species dominated. The current hegemony of calcareous nannoplankton in the world ocean results from a long-term and complex evolutionary history shaped by ecological interactions and abiotic forcing.</p>