The fluorescence in situ hybridization (FISH) which is a molecular method that allows phylogenetic identification of microorganisms in mixed assemblages from direct samples without prior cultivation, is based on the use of rRNA-targeted probes and works by means of epifluorescence, confocal laser scanning microscopy or flow cytometry. The sensitivity and specificity of FISH method are very high in prenatal diagnosis, cytogenetics biotechnology, molecular ecology and medical microbiology. The application of FISH method is easy and practical the cost per patient is less than PCR and conventional culture methods and the identification time is shorter (approximately 2 and 3 hours). This review is focused on classical FISH method that is applied for the rapid identification of microorganisms and its use (principle, method, advantage and disadvantages) in clinical microbiology.