Many techniques used in criminalistics, medical diagnostics, in phylogenetic studies and in organisms identification and differentiation are based on polymerase chain reaction (PCR). The choice of routine method to be applied routinely in a particular laboratory, is not easy and necessitate the knowledge and understanding of some one. In this paper, to facilitate the choice of the routine method for microorganism identification and differentiation, the detailed description of following methods is presented: RAPD (Randomly Amplified Polymorphic DNA), PCR-RFLP (PCR-Restriction Fragments Length Polymorphism), RISA (Ribosomal Intergenic Spacer Analysis), AFLP (Amplified Fragment Length Polymorphism), Multiplex PCR and Real-time PCR. The methods were compared by the most useful characteristics such as: application field, analysis repeatability, difficulty degree, analysis duration, automation possibility and cost.

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