The diet of free-living pinnipeds is most frequently estimated through identification of otoliths, squid mouth-parts and exoskeletons of prey in scats. This is because, although important prey types may not always be detected, sample collection is non-invasive and analysis is easy. Identification of prey DNA in scats is a nascent approach to determining the diet of marine vertebrates that may overcome some of the limitations of hard part analysis. This is the first study to experimentally compare the utility of genetic scatology for identifying consumption of prey types by seals with the occurrence of morphological remains of prey in scats. The occurrences of DNA and hard part remains of one squid and two fish taxa in scats of captive Arctocephalus seals fed mixed prey diets were compared. Both methods detected ingestion of these taxa 7.5–39.5 h prior to defaecation. Although all test prey had robust hard parts, detecting consumption during this period was 1.4 to 5.8 times more likely using genetic analysis than morphological analysis of scats. Based on frequency of occurrence calculations, neither method provided quantitative descriptions of the known diet. Identification of prey using DNA was not compromised by complexity of the diet; each test taxon was unambiguously detected against a background of a multi-species diet. Our results suggest that where diagnostic hard remains of prey are not well represented in scats, or the sample size is small, genetic scatology provides a valuable addition to morphological scat analysis for identifying the recent diet of free-living seals.