Diatoms play important roles in global carbon cycle supporting thus marine ecosystems. With more than 100,000 extant species, diatoms are considered as one of the most diverse and widespread phytoplankton in the world. In the current study, with the whole genome sequencing including illumina and Pac Bio of 17 accessions of the model diatom Phaeodactylum tricornutum which were sampled from different locations of the world oceans, we drew a complete and comprehensive landscape of the genomic and transcriptomic diversity within the species. We identified different growth rates, morphologies and cell size between the species as well as genetic subdivisions of the accessions with genome wide sequencing data providing further evidence and revisiting previously defined ecological niches. Finally, we show different transcription levels among these accessions using RNA sequencing and detected genes responsive to different growth parameters.  We built a framework defining a genetic structure of diatom populations in nature opening diverse perspectives to understand the biological characteristics of this model diatom species.