Methods for the extraction of DNA from water sample were approximated. Four different procedures of DNA extraction were carried out with pellets obtained from centrifugation of 4 liter water samples. The recovery efficiency and purity of DNA extracted by each method from different sources were compared. DNA yield varied with extraction methods, Method I, which involves enzymatic and freeze-thaw lysis steps and phenol and phenol-chloroform purification of extracted nucleic acid, showed a significantly higher yield and purity than the other methods. The use of glass beads in the DNA extraction methods improved the purity of DNA suitable for PCR. Bovine serum albumin in the PCR reaction mixture was useful in reducing inhibitory effects of contaminants. The efficiency of an extraction method was determined by the detection of the aer of Aeromonas hydrophila with PCR. The lower limit of detection of A. hydrophila from seeded tap water was 2 CFU/ml in PCR when method I was used for DNA preparation.