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Diatoms are one of the most abundant and diverse groups of phytoplankton and play a major role in marine ecosystems and Earth’s biogeochemical cycles. Here we combine DNA metabarcoding data from the Tara Oceans Expedition with palaeoenvironmental data and phylogenetic models of diversification to analyse the diversity dynamics of marine diatoms. We reveal a primary effect of pCO2 variation on early diatom diversification, followed by a major burst of diversification in the late Eocene, after which diversification is chiefly affected by sea level, an influx of silica availability, and competition with other planktonic groups. Our results demonstrate a remarkable heterogeneity of diversification dynamics across diatoms and suggest that a changing climate will favor some clades at the expense of others.