Despite widespread concern about biodiversity declines, few empirical studies exist on long-term population trends of mammal carnivores. In the context of global change, it is essential to understand the population trends and resource use of mammal carnivores. Mammal carnivores fulfil an important ecosystem function in terrestrial ecosystems as their top-down role directly and indirectly influences prey populations which affects the entire food web. The objective of this study was to evaluate whether and how the population trends of two sympatric mustelid species, stone marten and polecat, have changed between 1998 and 2013 in Flanders, Belgium. In addition, we explored temporal changes in their dietary habits. From 1998-2013, in collaboration with a citizen science network, we collected road-killed animals over the entire area of Flanders (13,682 km(2)). Based on the number of collected road-killed animals we detected a decrease in the polecat population during 1998-2013 whereas the stone marten population has increased. By subsequent identification of the stomach contents of the specimens, we detected fluctuations throughout the year of the consumption of certain food types. In addition, the consumption of certain food items decreased (stone marten: fruits, grains and nuts and lagomorphs; polecat: birds, rodents and other mammals) or increased (stone marten: edible waste and polecat: amphibians) throughout this period of opposite population trends. An increase of the degree of specialization of the diet throughout the sampling period was also detected for both mustelid species. In summary, our study concludes contrasting population trends coupled with clear changes in feeding habits of two sympatric carnivore species. Understanding these long-term relationships between species population trends and their dietary ecology is vital for biodiversity conservation and nature management.