This paper presents a comparative, diachronic study of the faunal assemblages recovered from two key political, cultural and commercial centres in the medieval Polish-Prussian borderlands: Kałdus in the Kulmerland, and Gdańsk in Pomerania. Both centres were situated in a region which was incorporated into the Teutonic Order’s state following the Crusades against the Prussian tribes in the 13th century. Although comparative trends are noticeable between the two centres which can be linked to the development of the Polish (Piast) state, the variation reflects specific local ecological and cultural contexts. Due to the constraints of space, this study focuses on the relative representation of different species of mammals, birds and fish, demonstrating how diachronic trends can be linked to the marked historical phases associated with the cultural and environmental transformation of this frontier, from one dominated by the Piast state to the later Teutonic Order’s polity.