DescriptionFor the last ~200 million years, two groups of unicellular eukaryotes have dominated the biomineralization of carbonate in the oceanic plankton: heterotrophic foraminifera and autotrophic coccolithophores. They literally transformed the fate of inorganic and organic carbon in the Earth’s biogeochemical system. The study of the evolution and biodiversity of these marine microcalcifiers has a long and venerable history, largely based on geological records and morphological characters. However, obtaining an accurate estimate of their biodiversity and understanding their evolution using only morphology and fossils is difficult due to issues such as dissolution, convergent morphology, and, for coccolithophores, the complicated haplo-diploid life cycle. Recent advances in molecular biology have further challenged the classic morphological studies by highlighting two additional problems: the unknown diversity of poor and non-calcifying forms in the global ocean and the widespread presence of cryptic species. The goal of this thesis was to reassess the evolutionary and ecological complexity of pelagic microcalcifiers at different taxonomic scales using molecular data constrained by morphological, ecological, and biogeographic metadata. I resolved the mode and tempo of the diversification of the haptophytes using an extensive multigene analysis and interpreted the timing of four key transitions in the evolution of the haptophytes in an ecological and geological context. I used Haptophyta-specific primers and PCR conditions adapted for GC-rich genomes to circumvent the biases inherent in classical genetic approaches. I discovered for the first time that the tiny (<3 µm) unicellular eukaryotes belonging to the haptophyte lineage are dramatically diverse in the planktonic photic realm, where they appear to dominate photosynthesis. I also developed a combined morphological-genetic approach to survey the environmental diversity of coccolithophores and evaluated the diversity level at which phylospecies and morphospecies can be considered equivalent concepts. Finally, I used the Neogloboquadrinids, a family of non-spinose planktonic foraminifera, as a model to assess cryptic speciation and global biogeography in the pelagic microcalcifiers.