Abstract: The transcriptomeof Skeletonema marinoi at different growth stages,different temperatures and low silicon concentration was analyzed with Illumina Hiseq 2000 platform sequencing technology,producing and identifying 39,098 transcripts totally.Assembled sequences were subjected to NR BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes orthology (KO) identifiers.These analyses identified the important metabolic pathways and genes of S.marinoi,especially the nitrogen metabolism pathway involving 20 enzymes and proteins.Comparative analysis of enzyme-coding genes among S.marinoi,Thalassiosira pseudonana and Phaeodactylum tricornutum using BLASTx revealed relatively high homologous genes between S.marinoi and T.pseudonana.Using the Digital Gene Expression Profiling,we also found different gene expression in the pathway.Compared to exponential growth phase (EP),three genes coding nitrate reductase or nitrite reductase which were involved in nitrate assimilation process showed significantly increasing expression in stationary phase (SP),as well as carbamoyl-phosphate synthase-coding and carbamate kinase-coding genes.The results indicated the molecular responses of S.marinoi on the nitrogen changes in different growth phases.Our study will contribute to analyze gene regulation of key enzymes involved in nitrogen metabolism of S.marinoi,providing a basis to enhance our knowledge about gene expression and regulation patterns in nitrogen limitation,which will be beneficial to in-depth understand the nutrients utilization in harmful algae bloom species.