Fatty acids (FA) analysis is a well-established approach for qualitatively studying feeding preferences. In the Argentinean Continental Shelf, Argentine hake Merluccius hubbsi supports the major demersal finfish fishery. The Patagonian stock of the species spawns and nurses in austral summer in the north Patagonian shelf (NPS, 43°–45°30′S). Previous studies about larval feeding in the NPS have solely focused on gut contents, indicating selectivity upon calanoid copepods. Hence, our main objective was to apply the FA approach to confirm and/or broaden M. hubbsi larval food selection. Hake larvae and copepod FA profiles overlapped significantly, dominated by the saturated FA 16:0, the monounsaturated FAs 18:1n-9 and 22:1n-9, and the polyunsaturated FA 22:6n-3. Moreover, identified markers typical of bacteria (15:0, 17:0) and dinoflagellates (18:4n-3, 22:6n-3) suggest a microbial input at the base of the NPS food web, with the latter probably acting as an intermediate step between bacteria and hake larvae. Possible direct predation upon protozoans by larvae is postulated, broadening the known trophic spectrum derived from classical diet analyses. The FA approach allowed us to clarify feeding preferences in the NPS, with data being relevant in the context of hake recruitment studies.