Molecular epidemiology (ME) is the application of molecular tools to determine the causation of disease. With infectious diseases, such as echinococcosis, this applies to identifying and characterising the aetiological agents and elucidating host range. Such an approach has been very successful with the causative agents of echinococcosis, species ofEchinococcus, initially by providing a workable and practical taxonomy and subsequently determining transmission patterns in endemic areas. This review summarises the taxonomy and nomenclature of species ofEchinococcusand provides an update on ME investigations of the ecology ofEchinococcustransmission, particularly in areas where more than one species ofEchinococcusis maintained in cycles of transmission that may interact.