Tick borne diseases are zoonoses causing infection in humans and domestic animals. The most spread zoonoses in Europe are the one caused by Borrelia burgdorferi sensu lato. Anaplasma phagocytophilum, Babesia spp., and Rickettsia spp. Impact of global, climatic and social changes occurring in recent years has increased incidence of ticks and number of infected people and animals. Movement of ticks into higher altitudes also causes the emergence of new foci. Our study was carried out in the Valle dei Laghi (northeastern Italian Alps). We have studied the prevalence and genetic variability of A.phagocytophilum and its ecological associations with hosts and vectors in the area. A total of 821 questing I. ricinus ticks were collected by dragging and 284 engorged ixodid ticks were collected from humans and from hunted or live-trapped wild-life animals. Further they were analyzed for the prevalence of A.phagocytophilum. All positive samples were used for amplification of groEL and msp4 genes for futher phylogenetic analysis. In addition 448 larve ticks from wild ungulates, birds and rodents were analyzed for reservoir competence for A.phagocytophilum, Babesia spp., B. burgdorferi s.l. and Rickettsia spp. Overall A. phagocytophilum prevalence in questing Ixodes ricinus ticks was 1.8%, in ticks from various host was: 4.3% in ticks from humans, 9.1% in ticks from dogs, 14.3% in ticks from wild ungulates, 7.7% in ticks from sheep, 10.7% in ticks from birds and 6.1% in ticks from rodents. Prevalence in rodent blood samples (A. flavicolis, M. avellanarius, M. glareolus) was only 0.3%. Phylogenetic analyses of msp4 and groEL showed two distinct enzootic cycles of A. phagocytophilum associated with different reservoirs as well as vectors. Strains that infect humans belong to the clade formed out of strains from engorged ticks collected from dogs, wild ungulates, sheep and birds. Strains obtained from rodents are most likely transmited by other tick vector and may not represent an immediate threat to humans in northern Italy. Our results shows different ecology of A.phagocytophilum as it is in United States. Moreover, from total of 339 engorged larvae I.ricinus ticks from rodents 9.1% were positive for B. burgdorferi sensu lato, 5.3% positive for Rickettsia spp. and 1.8% positive for Babesia spp. From 99 engorged larvae I.ricinus ticks from wild ungulates 6% were positive for A.phagocytophilum, 6% positive for Rickettsia spp. and 1% positive for Babesia spp. From 10 engorged larvae I.ricinus ticks from birds 80% were positive for B. burgdorferi s.l. High degree of genetic variability was observed. Our study revealed that in mountainous habitats of Norther Italy foci of tick-borne diseases are emerging. Small mammals and wild ungulates are the most important hosts for ticks as well as reservoirs for pathogens, however they participate differently in their ecology and circulation of tick borne agents in natural foci. The study was supported by the European Union grant FP7-261504 EDENext