Labeling and traceability of fish has become an important matter due to the need of safety and quality of food. Identification of commercially important fish species commercialized in the European market by means of molecular methods is a valuable work in order to prevent fraudolent substitutions and to set up traceability plans. Recent methods of molecular biology allow the detection of regions of the genome characterized by a different mutation rates and mutations that do not change the amino acid sequence. In this study, the TGGE (Temperature Gradient Gel Electrophoresis) and RFLP (Restriction Fragment Lenght Polymorphism) methods were used to identify fresh-water and marine species which are commonly available in the italian fish markets.