We studied the diet of the Great Cormorant Phalacrocorax carbo, during the release period of juvenile Chum Salmon Oncorhynchus keta, at two sites in southeastern Aomori Prefecture. To understand the prey and size of the cormorants, we analyzed stomach contents in early spring 2016, and to determine whether cormorants prey on juvenile salmon or not, we conducted DNA metabarcoding of cormorant feces in winter 2017/2018. Although stomach content analysis indicated that juvenile salmon were a suitable size for the cormorants, very little Salmonidae DNA was detected from fecal samples. We found that there was food differentiation between the two study sites, and that the diet of cormorants was reflected in their roosting locations. Some fishes such Grey Mullet Mugil cephalus, Japanese Sardine Sardinops melanostictus and Cyprindae species were found to be primary prey of the cormorants during the study period.