From continental to regional scales, the zoonosis alveolar echinococcosis (AE) (caused by Echinococcus multilocularis) forms discrete patches of endemicity within which transmission hotspots of much larger prevalence may occur. Since the late 80s, a number of hotspots have been identified in Europe and continental Asia, mostly in China, wherein the ecology of intermediate host communities has been described. Here we present a comparative natural history and characteristics of transmission ecosystems. On this basis, regional types of transmission and their ecological characteristics have been proposed in a general framework. Combining climatic, land cover and intermediate host species distribution data, we identified and mapped spatially distinct types of transmission ecosystems typified by the presence of 'flagship' intermediate host species. Each transmission ecosystem had its own characteristics which can serve as a reference for further in depth research in the transmission ecology of E. multilocularis. This approach may be used at fine spatial scales to characterize other poorly known transmission systems of the large Eurasian endemic zone, and help in consideration of surveillance systems and interventions.