The full-length cDNA sequence of phytoene synthase (PSY) encoding gene psy in Chlorella vulgaris (C. vulgaris)was isolated by RACE-PCR. The 1605 bp sequence contained a 1245 bp open reading frame (ORF), which encoded a protein composed of 415 amino acids residues. Results of multiple sequence alignment and phylogeny showed that the deduced protein sequence of the C. vulgaris PSY was homologous with other PSY proteins, and clustered into the green algae group. The genetic distances of PSY between C. vulgaris and Chlorella variabilis,Auxenochlorella protothecoides, Chromochloris zofingiensis was 0.173, 0.188 and 0.239 respectively. And those PSYs also kept the high similarity (81%-84%) and identity (69%-76%). The prediction result of subcellular location showed that the amino acids residues from 1^st to 45^th might perform as a chloroplast transit peptide, suggesting that PSY must be translated outside before entering the chloroplast and being active. Analyses of conserved blocks/motifs and tertiary structure modelling indicated that this PSY sequence contained several potential modification sites,with the conserved blocks and characteristic motifs of PSY protein, including two substrate-Mg²⁺ binding sites and two active site lid residues which might mediate binding of substrate and shield highly reactive intermediates from solvent. A specific substrate-Mg²⁺ binding site (the third) was found in the C. vulgaris PSY, and its activity and function was still unconfirmed.Taken together, these results uncovered the full-length cDNA sequence of psy, and predicted the putative structure of PSY protein in C. vulgaris, and thus provided information for over-expression of psy and for enhancing the productivity of carotenoids.