Scats (fecal samples) collected between 1987 and 2000 on northern fur seal Callorhinus ursinus rookeries of St Paul (n=2968) and St George Islands (n=1203), Alaska, were used to examine the relationship between breeding sites and food habits of adult female seals. On the basis of the frequency of occurrence (FO) and per cent minimum number of individual prey (%MNI) in scats, juvenile walleye pollock Theragra chalcogramma and gonatid squid Gonatopsis borealis/Berryteuthis magister and Gonatus madokai/Gonatus middendorffi were the dominant prey species consumed overall. Other primary prey (FO>5%) included Pacific sand lance Ammodytes hexapteus, Pacific herring Clupea pallasi, northern smoothtongue Leuroglossus schmidti, Atka mackerel Pleurogrammus monopterygius, Pacific salmon (Oncorhynchus spp.) and other squid of the Gonatus genus. We identified five rookery complexes from a cluster analysis of the FO of primary prey in scats. Rookery complexes were separated geographically and each was further defined by characteristic patterns in the representation of prey types typically associated with specific hydrographic domains. Diet differences were observed among rookeries on the north and south side of St George Island and on the east, south and south-west side of St Paul Island. The rookery clusters observed in this study provide evidence of resource partitioning among adult female northern fur seals and have important implications for fur seal conservation and management.