Calanus finmarchicus is the dominant zooplankton species in the North Atlantic. This zooplankton is also of interest for commercial harvesting due to its high abundance and biochemical contents. In the present study, copepodite stage V of C. finmarchicus was sampled at different depths from January to June in 2009, 2010 and 2011 in the Trondheimsfjord (63°29'N 10°18'E). The fatty acid composition was analyzed in individual copepods and in the seston. It was found that the fatty acid profile of copepods was related to the fatty acid profile of potential food sources. This study indicates that the onset of vertical migration of stage V, which was observed in May, has a strong link to the production of phytoplankton and lipid accumulation in C. finmarchicus. The content of 14:0 and 16:0 fatty acids in the specimens did not increase from February to May in surface waters. This suggests that these fatty acids in the diet were used as precursors for the biosynthesis of 20:1n-9 and 22:1n-11 fatty acids and fatty alcohols. A potential harvesting season of C. finmarchicus could be when the species is abundant in surface waters; the content of n-3 fatty acids will vary throughout this season. The peak abundance of C. finmarchicus in the spring varied substantially between the years studied.