Abstract: Desmodesmus sp. is an important green algae， which has the ability to produce interesting secondary metabolites， such as biodiesel and carotenoid. With the purpose to investigate the carotenoid biosynthesis pathway in Desmodesmus sp.， RNA-seq was employed to analyze the gene involved in the biosynthesis pathways. After sequencing and de novo assembly， a total of 37 634 Unigenes were obtained， 23 235 out of 37 634 Unigenes were annotated in at least one database， the most prominent GO categories （level 2） were metabolic process， cell part， and catalytic activity， respectively. 14 123 Unigenes were mapped to 128 biological pathways in the KEGG database. On the basis of the GO terms and KEGG annotation， candidate genes that encode enzymes involved in carotenoid biosynthetic were annotated， and the main carotenoid biosynthetic pathway was elucidated. The transcriptome provides a comprehensive sequence resource for the study of gene function and regulation of carotenoid biosynthesis pathways in this species.