Matrix attachment region (MAR) is DNA fragment that can bind to the nuclear matrix. In order to isolate the MAR fragment from the halotolerant green alga Dunaliella salina, we created a library of randomly obtained MAR from D. salina. Firstly the intact nuclei were released using 0.5% Triton X-100, then purification was carried out by discontinuous centrifugation using 30% and 70% Percoll gradients. Histones of nuclear matrices were removed using 25mmol/L lithium dioodosalicylate, the DNAs not closely associated with the matrices were removed using restriction enzymes. The remained matrices DNAs were digested by proteinase K, extracted with phenol/chloroform and precipitated with ethanol, and then cut with four kinds of restriction enzymes, the resulting DNAs were subsequently ligated to pUC18-vector and transferred to E. coli JM109 strains, DNA sequencing showed that the DNA fragments had the features of MAR DNA fragments.