Although studying the diet of threatened species is crucial in terms of conservation, the diet of the Madeiran Storm Petrel (Hydrobates castro) and the vulnerable, Azores-endemic Monteiro's Storm Petrel (H. monteiroi) is mostly unknown. The only information available to date comes from anecdotal observations, analysis of mercury levels and stable isotopes. Here is presented the first insights into prey consumption by adults and chicks from the two species breeding in the Azores Archipelago, Portugal, in the mid-Atlantic Ocean. The rapidly developing field of metabarcoding was used to identify dietary items from fecal samples, to species level where possible. A total of thirteen fish, five cephalopod, one crustacean and two oligochaete operational taxonomic units (OTUs) were detected. Results suggest that both petrel species feed mainly on myctophid fish. However, differences were detected between the prey species consumed by (i) H. monteiroi and H. castro, (ii) two distinct H. castro populations (Vila and Praia islets), and (iii) chicks and adults within the same population.