While the identification of microbial eukaryotes using molecular tools is now widespread, additional information are needed to confirm the molecular observation and make the difference between species and population variants, and therefore to better understand the biogeography of microbial eukaryotes. In this issue of Molecular Ecology, Postel et al (2020) not only used three molecular approaches to identify subgroups of Fragilariopsis kerguelensis but also morphology and physiology to better understand the relationship between the three genotypes. They revealed that (1) the three genotypes of the diatom F. kerguelensis have a negligible gene flux; and (2) two of the genotypes are geographically isolated with different physiology but still able to crossbreed; and (3) the last one is omnipresent but reproductively isolated.