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International audience; Phaeodactylum tricornutum is the most studied diatom encountered principally in coastal unstable environments. It has been hypothesized that the great adaptability of P. tricornutum is probably due to its pleomorphism. Indeed, P. tricornutum is an atypical diatom since it can display three morphotypes: fusiform, triradiate and oval. Currently, little information is available regarding the physiological significance of this morphogenesis. In this study, we adapted P. tricornutum Pt3 strain to obtain algal culture particularly enriched in one dominant morphotype: fusiform, triradiate or oval. These cultures were used to run high-throughput RNA-Sequencing. The whole mRNA transcriptome of each morphotype was determined. Pairwise comparisons highlighted biological processes and molecular functions which are up-and down-regulated. Finally, intersection analysis allowed us to identify the specific features from the oval morphotype which is of particular interest as it is often described to be more resistant to stresses. This study represent the first transcriptome wide characterization of the three morphotypes from P. tricornutum performed on cultures specifically enriched issued from the same Pt3 strain. This work represents an important step for the understanding of the morphogenesis in P. tricornutum and highlights the particular features of the oval morphotype. Diatoms are a major component of phytoplankton communities. They belong to a group of unicellular heterokont microalgae expected to include at least 200,000 species 1. Their genomes contain unique combinations of nutrient assimilation and metabolic pathways which have been attributed to their origin 2. Indeed, diatoms derived from a serial secondary endosymbiotic event in which a green algae and subsequently a red one were engulfed by a heter-otrophic eukaryote 3-5. Among the diatom species, Thalassiosira pseudonana (T. pseudonana) and Phaeodactylum tricornutum (P. tricornutum; Pt) have been chosen based on the number of research groups working on them and genome size considerations 6-8. The comparative analysis of T. pseudonana and P. tricornutum genomes highlights the presence of 10% of diatom specific genes which have no homologs in other eukaryotes 6,7,9. In addition, it has been demonstrated that P. tricornutum and T. pseudonana possess 6.4% and 2% of transposable elements, respectively 6,7,10 as well as microRNAs 11,12. Moreover, a recent re-analysis of the P. tricornutum genome revealed that among 251 different patterns identified across the entire genome, many genes have limited evolutionary conservation with 47% having originated within the recent vertical history of the stramenopile lineage and a total of 26% of genes (3170 genes) being specific to P. tricornutum 8. P. tricornutum is probably the widest studied diatom. Its genome has been sequenced and a large scale tran-scriptomic analysis has been recently published 7-9. It is a cosmopolitan diatom not widely distributed in nature, but is encountered principally in coastal unstable environments such as estuaries or rock pools 13,14. Moreover, P.