The aim of my PhD project was to investigate the molecular mechanisms underlying Hydra regeneration. I approached this question mainly through transcriptomic analysis, namely RNA-seq thanks to Next Generation Sequencing. In spite of more than 250 years of accumulated research on its regenerative potential, the Hydra model system was yet to benefit from the recent development of high throughput sequencing methods. The Hydra genome was recently made available, however a global perspective of the genes expressed in Hydra was missing and thus several important biological questions that extend beyond the Hydra model system were difficult to address. In an attempt to fill this gap, we applied RNAseq to focus on three aspects: i) produce an inventory of the genes expressed in Hydra vulgaris, ii) analyze the evolution of proteomes among metazoans, iii) characterize the transcriptional modulations along the Hydra body axis and in regenerative contexts.