Fatty acid biomarker analysis of the Cyclopoid copepods Oithona similis and Oithona frigida sampled from the Southern Ocean during the austral summer has indicated differences in diet between the two species. Oithona similis contained higher proportions of protozoan and bacterial fatty acids markers, indicative of microbial foodwebs involved in the recycling of detrital material and faecal pellets. In contrast, the fatty acid composition of O. frigida was characterized by a strong diatom signature. Despite these species-specific differences, the fatty acid biomarker composition of both species at each of the stations sampled primarily reflected the species composition of the microplankton in their environment. Comparison of an index of fatty acid composition with nutritional condition indicated that those CV and female O. similis containing the highest levels of diatom biomarkers fatty acids were in the best condition. These findings suggest that diatoms are more important for Oithona spp. in the Southern Ocean than for other oceanic regions and are consistent view that O. similis is an integral component of food webs associated with the recycling of detrital aggregates and faecal material.