The blue sponge Xestospongia sp. was found to produce the potent cytotoxic renieramycin alkaloids. It is motivating to study renieramycin biosynthesis to produce these compounds by biotechnology. To primarily answer the biosynthesis question, genetic DNA materials with good in both quantity and quality are required. A commercial kit for DNA extraction from the sponge samples was compared with other six protocols reported in literatures. The quality and the total yield of obtained DNA were estimated by measuring the absorbance ratio (OD₂₆₀/OD₂₈₀) and absorbance at 260 nm (OD₂₆₀), respectively. The most appropriate protocol for DNA extraction from the marine blue sponge Xestospongia sp. is the NaOAc salting-out protocol. The NaOAc salting-out protocol was selected for further modification to improve DNA extraction from the sponge Xestospongia sp. by optimizing lysis buffer solution compositions, salt solution for protein precipitation, DNA precipitation method, and addition of RNase enzyme. The DNA quantity and purity from the modified protocol were significantly better than those from the original protocol. The modified protocol was remarkably suitable for DNA extraction from the blue sponge Xestospongia sp. more than other organisms and was specifically named as the blue sponge Xestospongia sp. DNA extraction protocol. Finally, to investigate DNA quality in molecular study aspect, PCR amplifications were performed. The amplicons amplified by 28s rRNA and COX I genes of Xestospongia genome were in expected size. Further DNA sequence analysis showed that the amplicons for COX I gene in the database. All the results revealed that the blue sponge Xestospongia sp. DNA extraction protocol was a preferable procedure to extract Xestospongia sp. DNA for further molecular biology study.