The present invention relates to a screening method for a drug target gene by using chemical-genetic profile compendium of the heterozygous deletion fission yeast strain and the comparative genetic analysis using the same. More precisely, the present inventors constructed the chemical-genetic profile compendium for drug candidates from the heterozygous deletion fission yeast strain of Schizosaccharomyces pombe (S. pombe), and then compared with the compendium with the chemical-genetic profile compendium of the budding yeast Saccharomyces cerevisiae (S. cerevisiae) in order to select efficiently drug target genes showing drug sensitivity. The screening method of the present invention can be efficiently used for the identification of a drug target gene in various eukaryotes because it facilitates the selection of a drug target gene showing sensitivity to the drug from the chemical-genetic profile compendium of the heterozygous deletion fission yeast strain.