Combined analyses of Fatty Acid Trophic Markers (FATM) and Stable Isotopes (SI) were used to characterize food preferences among copepod species/taxa and to trace their food sources in the ultra-oligotrophic Cretan Passage of the Eastern Mediterranean Sea (EMS). FATMs are based on the conservation and transfer of specific source Fatty Acids (FAs) through the food web, providing a qualitative indicator of assimilated food types. SI provide information about trophic levels and food sources of specific organisms. Most species/taxa exhibited low δ15N ratios caused by low δ15N-PON base values at the study site. A cluster analysis based on the mean Fatty Acid (FA) compositions of nine copepods from all stations identified three distinct groups (group 1: Clausocalanus lividus and Euchaeta spp.; group 2: Pleuromamma spp., Haloptilus longicornis, Lucicutia spp., Clausocalanus spp. and Corycaeus spp.; group 3: Pareucalanus attenuatus and Oncaea spp.), coinciding with similarities in feeding behavior. H. longicornis, however, revealed similar trophic positions but different food resources by FATM and SIA analyses. Overall, we conclude that omnivory was the prevailing feeding mode, demonstrating a high degree of opportunistic feeding of copepods in these ultra-oligotrophic waters. This study shed first light on the zooplankton taxa/species life strategies with regard to feeding preferences and lipid storage mechanisms in the oligotrophic EMS, where lack of relevant information exists. Although further investigation is required, the good agreement between FA and SI in some species of copepods emphasize the applicability of lipid trophic markers. Results benefit from the coupling of these indices even in oligotrophic regions of the world ocean.