The present invention relates to a method so called Bacterial Digitalcode System (BaDis) that identifies microorganism by using bacterial-specific, genus-specific and species-specific oligonucleotides from a variety of samples or specimens for detection and differential diagnosis of microorganism. Particularly, the present invention relates to bacterial-specific, genus-specific and species-specific oligonucleotides designed by the target nucleotide sequences of 23S rDNA or ITS gene, polymerase chain reaction (hereinafter, referred to as "PCR") kits using the oligonucleotides as a primer, the microarray containing the oligonucleotides as a probe, and methods for detecting microorganism by using the oligonucleotides. Therefore, the present invention can be applied to detect the presence of microorganism and diagnose differentially all microorganism such as pathogenic bacteria of infectious diseases, bacteria inducing food poisoning, bacteria contaminating biomedical products and environmental pollutants.