Anisakid nematodes commonly infect gadids, and are of economic and aesthetic importance to the commercial fishing industry in Greenland as some species are pathogenic to humans. However, very little is known about the occurrence of these parasites and their impact on the hosts in Greenland waters. During a survey in 2005, stomach sample of 227 Atlantic cod (Gadus morhua) and 64 Greenland cod (Gadus ogac) was collected in Godthaab and Sisimiut fiord systems in West Greenland waters. All cod were dissected for stomach contents and anisakid nematodes were removed from the visceral cavity. Third stage larvae (L3) of three anisakid species were found, including Contracaecum osculatum (Rudolphi, 1802), Anisakis simplex (Rudolphi, 1809) and Hysterothylacium aduncum (Rudolphi, 1802). Molecular identification by PCR-RFLP indicated the presence of A. simplex s.s. and the sibling species C. osculatum B and C. The prevalence of infection by C. osculatum was higher in Greenland cod (84.3%) than in Atlantic cod (73.9%) whereas the prevalence of A. simplex showed an opposite pattern (Greenland cod 8.3%; Atlantic cod 24.2%). Only one G. morhua (1.0%) was infected by H. aduncum. No gender specific difference in both nematode species regarding prevalence of infection and mean infection intensity was evident, and there was no relationship between fish condition and the intensity of nematode infections. Standardised for size, capelin-eating cod were in better condition and more heavily infected than fish subsisting on alternative prey at the point of collection. Hence, nematode infections in the two gadids seem governed in part by feeding behaviour, and capelin appears a significant source of larval anisakids.