Molecular epidemiology can be defined as an integrated approach that combines epidemiology and biotyping using molecular biology tools. As such it is an hybrid discipline and any molecular epidemiology study should obey the basic principles of both epidemiology and molecular typing. The sampling frames and gathering of epidemiological data should allow a statistical analysis of the results as the molecular biology tools should have a good repeatability as well as a good discriminating power below the species level. The choice of one or multiple techniques will naturally depend on the biodiversity that exists among the species to be considered. This biodiversity is the result of the evolution of populations of strains with bacterial species being seen as "condensed nodes" in a cloudy space. In the long term, it is expected that whole genome sequencing will become the ultimate tool for strain characterization. Until then, suboptimal techniques have to be used and the choice of the technique will have to be taylored for each mycoplasma species and for the specific objective of the study. Among the various techniques that can be used for the molecular typing of Mycoplasmas, some require the isolation of the strains and DNA extraction. This is the case for pulsed field gel electrophoresis, restriction endonuclease analysis, Southern blotting, random amplification of polymorphic DNA or amplified fragment length polymorphism. Other techniques do not require the isolation of the causative organism as they are based on PCR followed by an enzymatic restriction analysis or sequencing. Ultimately multiple loci can be amplified and sequenced in order to increase the discriminatory power of the technique. It is hoped that the integration of epidemiological studies with fine molecular typing will induce a better knowledge on the dynamics of of mycoplasma strains evolution and spread and, finally, allow a better evaluation of risk and better definition of disease control strategies