The feeding ecology of the Great Cormorant Phalacrocorax carbo has been the subject of many studies in which the hard parts of fish, contained in dietary samples such as regurgitated pellets, were identified using morphological characteristics. However, morphological prey identification does not necessarily permit the reliable identification of all fish species due to digestion eroding diagnostic characters and/or morphologically indiscernible hard parts in a range of fish species. Molecular methods have the potential to overcome these obstacles by allowing the detection and identification of minute quantities of prey DNA present in pellets, faeces, and stomach samples. Moreover, DNA of the consumer (i.e. the Cormorant) is also present in dietary samples and can thus be employed for ecological studies too. Here, we present a methodological overview of two molecular approaches commonly used to study trophic interactions, namely diagnostic PCR and next generation sequencing, along with their main advantages and disadvantages. Regarding the use of consumer DNA contained in dietary samples, molecular sexing, i.e. the non-invasive sex determination of the sample-producing bird, is presented. We exemplify the potential of DNA-based methods for future research via a case study on pellets collected at Chiemsee (Germany), which were subjected to molecular and morphological prey identification as well as to molecular sexing. Compared to morphological prey identification, molecular analysis led to a 53% increase in prey species and genera, mainly caused by eight additionally detected cyprinid taxa. For 79% of the pellets, the sex of the pellet-producing Cormorant could be successfully determined via molecular sexing. Our findings highlight the exciting possibilities molecular methods offer for future studies on Cormorant feeding ecology, especially regarding evaluations of prey spectra and the non-invasive assessment of sex-specific differences.