In this study, the transcriptome of the marine microalga, Chlorella pyrenoidosa 820, was sequenced by high-throughput RNA-seq using Illumina HiSeq 2000. Because the genome sequence of this species is unknown, the resulting transcriptome was assembled de novo and annotated. This resulted in 4.71G clean nucleotides with a 56.91% GC content and yielded a total of 36,826 unigenes with a mean length of 1089 nt. Among these, 23,015 unigenes were annotated in the NCBI-NR, NCBI-NT, Swiss-Prot, KEGG, COG, and GO databases with a cutoff E-value of 10 -5 . In the annotated sequences, 21 unigenes were identified as carbonic anhydrase (CA), which is an important enzyme in the CO 2 -concentrating mechanism (CCM), and were homologous to nine α-, eight β-, and four γ-CAs. Interestingly, the expression of three CA subtypes, including one α-, one β-, and one γ-CA, analyzed by real-time quantitative PCR, showed induction by high salinity. These results will enrich the CA gene information in the database and will help understand CCM in the genus Chlorella .