Filamentous Cyanobacteria commonly has mucilaginous sheath as cells' protection from any physical damage, such as dehydration or UV-light. In many experiences, the presence of sheath in the process of DNA extraction caused low concentration and purity of DNA samples. In order to optimize DNA extraction for species identification, a method called heat shock was used in present study. In general, heat shock refers to cellular exposure to rapid stress changes such as temperature. Three strains of Cyanobacteria from genus Nostoc (SO-24), Cylindrospermum (SO-163), and Fischerella (SO-133) were used as samples based on their characteristic of mucilaginous sheath. Three variations of temperature were used in present study: 50, 80 and 100 °C. The DNA yield and purity for the method were evaluated using spectrophotometry and compared. The results showed that DNA extraction gained maximum DNA concentration at temperature of 50 °C. Temperature did not have a correlation with DNA purity of the samples. Each strain had different response to the method and this might be because the thickness of the sheath on each strains.