Species identification is the basis of Biology and has been carried out based on phenotype. Although some genes, such as that for 16S rRNA, have been used for species confirmation, identification of species based only on genotype has never been done before, although recent whole genome sequencing studies have demonstrated it to be possible in principle. However, it is evidently unrealistic for routine experiments of species identification. This paper clarifies that a very limited amount of information derived from a genome sequence is sufficient for identifying the species. It also proves that Genome Profiling [Nishigaki, K., Amano, N., and Takasawa, T. (1991) Chem. Lett. 1097-1100], TGGE analysis of random PCR products, can not only fulfill such requirements, but also serve as a universal method to analyze species. Thus, this compact technology can be used in many fields of biology, especially in microbe-related disciplines such as microbial ecology and epidemiology where exact knowledge about all members of a population is essential but previously difficult to obtain. This is the first demonstration that genotype-based identification of species is possible using a simple and uniform protocol for all organisms.