Chloroplast genomes of algae display a large variation in structure,many species absence of IR region and show that IR is not a necessary region for algae.Chloroplast genomes of algae have more genes and an increased coding capacity relative to land high plant chloroplast genomes.Fosmid library is a highly useful approach for obtaining chloroplast genome sequences.Long-PCR can be used to amplify large fragments of the genome using conserved chloroplast primers.The paper introduced the structure and genes of chloroplast genome,chloroplast DNA systematics,isolation of pure cpDNA and whole cpDNA sequencing methods,that may provide the theory basis for research of algal phylogenetics and origin of chloroplast.