The fishpond landscapes in Central and Eastern Europe have immense historical and cultural value, and are highly significant as a habitat for numerous endangered species. Typical examples of cultural landscapes, their maintenance depends on (extensive) fishpond farming. However, although the protection of endangered pescivore predators in these landscapes such as the otter and the cormorant has been successful in recent years, it is increasingly running into conflict due to the damage caused by these species in the fishponds. We present a comparative analysis of such conflicts with otters in two regions with a long history of carp-farming Upper Lusatia in Saxony (Germany) and South Bohemia in the Czech Republic. For this purpose we examine various ecological, economic and social aspects of the conflicts in both regions. We compare the recent socioeconomic developments, explore fish-farming practices, and investigate factors likely to influence conflict perception and manifestation. Based on the comparative analysis and drawing on other relevant literature, the problem of biodiversity conflict characterisation is analysed in terms of the extent of a conflict and its dynamics. In this context, basic difficulties of designing and evaluating conflict mitigation measures are discussed.