A method for DNA extraction from sediment samples of Lake Xuanwu, Nanjing, China was developed, and purification and efficience of extracted DNAs were evaluated through ultraviolet spectrum OD₂₆₀/OD₂₈₀ ratios and PCR ampliilcation of 16S rDNA specific for Microcystis. The results showed that sediment samples from all sites in the study obtained quite purified genomic DNAs with OD₂₆₀/OD₂₈₀ ratios from 1.54 to 1.89, and Microcystis 16S rRNA gene fragments have been detected in all sampling sites, which indicating this method can be used for molecular detection of Microcystis cells in sediments.