RAPD molecular method is the Expressed Sequence database was used as the original genomic information for identification of polymorphic sites. Primers OPW-04, 05 and 06 RAPD is designed and the amplified PCR products are then directly sequenced. All sequences obtained are aligned to search possible RAPD altering the restriction enzymes recognition sites. At last, the method is used to genotype of these RAPD markers in large population samples of the of chlorococcales species complex. The physico-chemical parameters like phosphate and nitrate exhibit a positive correlation with the dynamics of chlorococcales. The results showed that 70, 69 and 75 RAPD bands with Primer OPW-0showed geographical discrimination. Molecular markers in algae and can be more relevant than other neutral markers mentioned above due to the high occurrence of RAPD in their functional genomic regions. Because of the potential for higher genotyping efficiency, data quality, genome-wide coverage, and analytical simplicity, RAPD have been used as molecular markers in evolutionary and ecological studies of a wide range of organisms in the current study, we report the characterization of 19 species of ofchlorococcales4, OPW-05 and OPW- 06are useful for genetic diversity studies of chlorococcales as they.

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