The gephyrocapsids are a species complex that often dominate coccolithophore assemblages and calcification in the ocean. These unicellular phytoplankton are known to produce calcite plates of variable size for optimal adaptation to their environment. High-resolution (~2-3 kyr) records of coccolith size and mass measured in 12 tropical cores spanning up to 2.8 million years show regular and recurrent variations that follow the rhythms of the eccentricity of Earth’s orbit. This rhythmic pattern is different to records of long-term variation of global climate impacted largely by ice-volume. Instead, we posit that it reflects the amplitude of the low-latitude seasonal contrast under the direct influence of eccentricity. These seasonal dynamics of the ocean are masked in most paleoceanographic records of the last million years by the large variations of global ice volume and their influence on climate. However, similar pattern in the changes in amplitude of some climate proxies can be seen (d18Oatm, monsoon proxies, ocean productivity). These seasonal dynamics, although rarely documented, were strong enough to change the distribution of oceanic ecological niches in the ocean and thus drive coccolithophore evolution.