The aim of this study was to investigate spatial changes in the trophic and energy pathways of the benthic community in the shallow shelf waters of the sub-Antarctic Prince Edward Islands (PEI). A combination of stable isotope and fatty acid analyses were used to provide a time-integrated view of the assimilated feeding history of selected components of the PEI benthic community. This study forms part of the larger project entitled “Variability in the Southern Ocean ecosystems” and is a contribution to the South African National Antarctic Programme (SANAP). During austral autumn 2009, benthic specimens were collected from 10 stations (from depths of 70 to 295 m) in different regions around the PEI: inter-island shelf (upstream, between and downstream of the islands) and nearshore. Historical data were combined with new data collected during 2009 to assess the long-term trends in the feeding ecology of the benthos in the region of the islands. The stable isotope and fatty acid signatures of the benthic suspension- and deposit-feeding organisms generated during this study suggested that these two communities incorporated both phytoplankton and kelp in their diets. Stable isotope, and to a lesser extent fatty acid signatures, indicated that kelp contributed more to the diets of those organisms in close proximity to the kelp beds (nearshore stations) than those from the inter-island region. Overall, however, pelagic phytoplankton was the dominant food source in the diets of all organisms, even for those living near the kelp beds. Notable exceptions were the sponges and bryozoans, in which kelp and phytoplankton contributed similar proportions to their diets, most likely resulting from a size restricted feeding mode. There were, therefore, no distinct spatial differences in the importance of the various food sources. However, fatty acid compositional data indicated increased food quality between and within the lee of the islands compared to upstream. The organisms collected upstream of the PEI had substantially lower quantities of total fatty acids (TFAs) than organisms of the same species collected from nearshore, open shelf or downstream stations. The increased food quality between and within the lee of the islands was likely a result of the “island mass effect”, which reflects increased phytoplankton concentrations at the PEI. The fatty acid profiles of hyperbenthic shrimp Nauticaris marionis, a key species in the PEI ecosystem, revealed no distinct ontogenetic or spatial patterns. This result is in contrast to the stable isotope analyses, which detected both spatial and ontogenetic differences in the diet of the shrimp. Nearshore shrimp were more ₁₃C-enriched than those from the inter-island region, suggesting increased kelp entering the food web within these regions. In addition, the shrimps demonstrated enrichment in δ₁₃C and δ₁₅N signatures with an increase in size, resulting in a relatively distinct separation of size classes, thus reflecting niche separation through their diets. The fatty acid profiles revealed that the shrimp all contained large proportions of polyunsaturated fatty acids (PUFAs) and essential fatty acids (EFAs), indicating that the quality of food consumed was similar among size class and region despite the niche separation and variation in carbon sources utilised. In addition, diatom and dinoflagellate fatty acids (20:5ω3 and 22:6ω3, respectively) occurred in the highest proportions in N. marionis, highlighting the importance of phytoplankton (indirectly) in their diet. These results represent strong evidence that phytoplankton is an importance food source in the PEI ecosystem. The temporal investigation of isotope signatures in the benthos at the PEI indicated that N. marionis demonstrated an overall depletion in δ₁₃C signatures over the period of 1984 to 2009 (nearshore: -2.55 ‰, inter-island: -2.32 ‰). Overall, the benthic community showed similar depletions in δ13C signatures (from -1.96 to -4.70 ‰), suggesting that shifts have occurred in the carbon signatures at the base of the food web. The depletion in δ₁₃C signatures of the benthos at the PEI most likely reflects increased contributions of smaller slow growing phytoplankton cells (more depleted signatures than large fast growing cells) in the diets of these organisms over time. These diet shifts, in turn, suggest a decrease in productivity has occurred at the islands, likely due to a decreased frequency and intensity of the “island mass effect”. Decreased phytoplankton productivity at the PEI likely results from the southward shift in the average position of the sub-Antarctic Front (SAF), most likely in response to climate change, which in turn promotes flow-through conditions rather than retention at the PEI.