Since lots of antifreeze proteins exist in Antarctic fishes, it is quite difficult to acquire high quality genomic DNA by using normal genomic DNA extraction method. In order to establish an effective genomic DNA extraction technique for Antarctic fish, one kind of Antarctic fish, Trematomus bernacchii, was used as the experimental material, and three different kinds of genomic DNA extraction methods (the modified phenol chloroform method, normal phenol chloroform method and the genomic extraction kit method) were compared. The acquired genomic DNA was appraised by spectrophotometer, agarose gel electrophoresis, and PCR amplification. The results showed that we successfully obtained high quality genomic DNA from T. bernacchii by using our modified phenol chloroform method. The gel bands were very neat and bright, the ratio of A260/A280 was around 1.80, and the acquired genomic DNA was suitable for PCR experiments. In a word, the extracted genomic DNA by using our modified phenol chloroform method, was in good quantity and suitable for the PCR based molecular experiment.