Microorganisms drive the global carbon and nutrient cycles that underlie essential ecosystem functioning. Yet, our understanding of microbial speciation, evolutionary history and biogeography remains elusive. Especially terrestrial protists are heavily understudied. Given the rapid and irreversible environmental changes affecting the Polar Regions today, this knowledge-gap is critical for the Arctic and Antarctic, where terrestrial microalgae dominate biodiversity. Here, I will combine large-scale phylogenetic and population genetic studies of the terrestrial diatom species complex Pinnularia borealis, with a strong focus on the Polar Regions. Specifically, I will (i) create a phylogenomic framework of the P. borealis complex to study levels of ancient introgression and patterns of positive selection related to the colonization of polar environments, (ii) investigate population structure, gene flow, and mode of speciation in a bipolar P. borealis species, and (iii) study ancient DNA to investigate Late-Pleistocene and Holocene dynamics in Antarctic P. borealis species and populations, and the impact of glacial/interglacial cycles thereon. This project will provide novel insights into the drivers of species- and population-level diversity of a diatom species complex, and how this is affected by past environmental change. As such, the results will serve as a model for understanding the evolutionary history of both terrestrial microalgae and polar terrestrial diversity.