In Europe, Anaplasma phagocytophilum is an emerging tick-borne pathogen with both medical and veterinary importance, being the causative agent of human granulocytic anaplasmosis (HGA) and the tick-borne fever of domestic animals. Its ecology and its molecular diversity in Europe is currently under assessement. Therefore, we analyzed and compared the genetic variability of different A. phagocytophilum strains identified in feeding ticks collected from roe deer, rodents, birds, sheep’s, dogs from Trentino region of Northern Italy. Furthermore, prevalence of other pathogens of public health importance such as Babesia sp., Borrelia sp. and Rickettsia sp. was also estimated.