Molecular tools are used increasingly for descriptive epidemiological studies in different Mediterranean foci of visceral and cutaneous leishmaniases. Several molecular markers with different resolution levels have been developed to address key epidemiological questions related to the (re-)emergence and spread of leishmaniases, as well as its risk factors: environmental changes, immunosuppression and treatment failure. Typing and analytical tools are improving but are not yet addressing all epidemiological issues satisfactorily. There is an urgent need for better cooperation between laboratory scientists and epidemiologists and for regional epidemiological surveillance of these infectious diseases that affect all Mediterranean countries.