AbstractTo reduce the use of chemical fertilizers and maximize agricultural yields, the use of microalgae extracts as biostimulants has recently attracted significant attention due to their favourable impact on both plant growth and their ability to induce tolerance towards environmental stressors. Lettuce (Lactuca sativa) is one of the most important fresh vegetables that often requires applications of chemical fertilizers to increase quality and productivity. Accordingly, the purpose of this study was to analyse the transcriptome reprogramming of lettuce (L. sativa) seedlings in response to eitherChlorella vulgarisorScenedesmus quadricaudaextracts by applying an RNAseq approach. Differential gene expression analysis revealed that the core gene set that responded to microalgal treatments in a species-independent manner includes 1330 clusters, 1184 of which were down-regulated and 146 up-regulated, clearly suggesting that the repression of gene expression is the main effect of algal treatments. The deregulation of 7197 transcripts in theC. vulgaristreated seedlings compared to control samples (LsCv vs.LsCK) and 7118 transcripts in theS. quadricaudatreated seedlings compared to control samples (LsSq vs.LsCK) were counted. Although the number of deregulated genes turned out to be similar between the algal treatments, the level of deregulation was higher inLsCv versusLsCK than inLsSq versusLsCK. In addition, 2439 deregulated transcripts were observed in theC. vulgaristreated seedlings compared toS. quadricaudatreated samples (LsCv vs.LsSq comparison) suggesting that a specific transcriptomic profile was induced by the single algal extracts. ‘Plant hormone signal transduction’ category includes a very elevated number of DEGs, many of them specifically indicating thatC. vulgarisactives both genes involved in the auxin biosynthesis and transduction pathways, whereasS. quadricaudaup-regulates genes implicated in the cytokinin biosynthesis pathway. Finally, algal treatments induced the deregulation of genes encoding small hormone-like molecules that are known to act alone or by interacting with major plant hormones. In conclusion, this study offers the groundwork to draw up a list of putative gene targets with the aim of lettuce genetic improvement that will allow a limited or even null use of synthetic fertilizers and pesticides in the management of this crop.