Changes in climate and exploitation have caused large fluctuations in the productivity of many North Atlantic cod populations and the collapse of many cod fisheries. These fluctuations are most likely due to a combined effect of physical processes and changes in ecosystem trophic structure. To study the link between environmental changes and ecosystem trophic structure we developed δ15N and δ13C chronologies by analyzing the organic matrix of cod otoliths from the Faroe Shelf cod population (1950-2010) and the Nuuk Fjord cod population (1927-2009). Significant correlations between δ15N & δ13C annual mean values over time were seen in both ecosystems, suggesting δ15N & δ13C values were affected by the same overall processes. There were significant effects of climate variables (temperature, Atlantic Multi-decadal Oscillation (AMO) and Sub Polar Gyre index) on δ15N and δ13C chronologies in both ecosystems. Fast Fourier Transformations showed the same periodicity in climate variables, δ15N and δ13C chronologies and cod size-at-age. In the Nuuk Fjord ecosystem discontinuity analyses (STARS) found coinciding shifts in both δ15N & δ13C chronologies, climate variables, cod size-at-age and inshore cod catches. This indicates a large ecosystem shift in the Nuuk Fjord around 1970 and a smaller in 1995 and is further supported by the δ15N & δ13C bi-plot that shows a clear separation in signatures before and after 1970. To separate baseline shifts from trophic shifts new δ15N and δ13C chronologies of organic matrix of otolith core material (Nuuk Fjord) and annual growth increments in Ocean Quahog (A. Islandica) shells will be included.