Molecular typing and fingerprinting of bacterial pathogens has become a major part of epidemiology, disease monitoring, intervention and food safety research. This treatise will briefly address the aims of molecular typing and the criteria that are important to choose the optimal method of typing. However, since the method of choice will depend on a number of factors, including available facilities and research goals, no particular methods are recommended; instead, theoretical considerations are presented as a guide line for the best decision. Since molecular typing is examining the nature of the population genetics of a particular organism, it is important to understand how the degree of clonality of that particular organism will influence outcome and interpretation of results. The mechanisms that lead to non-clonality are briefly outlined. The problems with typing of clonal, non-clonal, and weakly clonal populations are briefly treated. The merits and myths of multilocus sequence typing (MLST) are discussed.