Birds are important in the maintenance and spread of ticks and tick-borne diseases. In this context we screened birds in the Atlantic forest north of the São Francisco River and Caatinga in northeast Brazil. In the Atlantic forest Amblyomma longirostre, Amblyomma nodosum, Amblyomma varium and Amblyomma auricularium were identified. A. longirostre was infected by “Candidatus Rickettsia amblyommii” and A. nodosum by a Rickettsia parkeri-like agent. In Caatinga, Amblyomma parvum and A. auricularium were identified. A. auricularium was infected by “Ca. R. amblyommii” and Rickettsia bellii. “Canditatus Rickettsia andenae” was also identified in A. parvum collected from birds in Caatinga. In addition, Rickettsia sp. genotype AL was identified in A. varium collected on the clothes of the field team in one area of Atlantic forest. Here we provide a series of new host records for several Neotropical Amblyomma species and document rickettsial infections of “Ca. R. amblyomii” and a R. parkeri-like agent in Paraíba State, and R. bellii and “Ca. R. andenae” in Bahia State. For the first time we provide information regarding the infection of A. varium by “Ca. R. amblyommii”.