An isolation structure in a memory device and a method for fabricating the isolation structure. In the method, a first trench is formed in a cell region of a semiconductor substrate and a second trench in a peripheral region of the semiconductor substrate. A liner layer comprising a silicon nitride layer is formed on the first and second trenches. A spin on dielectric (SOD) layer comprising polysilazane is formed on the liner layer so as to fill the first and second trenches. A portion of the SOD layer filling the second trench is removed. A portion of the silicon nitride layer, which is disposed on the second trench and is exposed after the removing of the portion of the SOD layer, is oxidized using oxygen plasma and heat generated from the plasma. A high density plasma (HDP) oxide layer is formed to fill the second trench.