A population of small-sized Arctic charr living their entire life cycle in deep water was recently found in Lake Skogsfjordvatn, Northern Norway. Their phenotype and life history closely resembles the profundal charr morph in another subarctic Norwegian lake, Fjellfrosvatn. Fjellfrosvatn has one littoral omnivorous and one small profundal benthivorous (PB) charr morph coexisting with brown trout, whereas Skogsfjordvatn has migratory salmon, trout, charr and eel populations in addition to threespined sticklebacks, resident trout and three resident charr morphs of which one is a large piscivorous profundal morph. We predicted that the small profundal charr morph in Skogsfjordvatn would have a similar trophic niche to the PB-morph in Fjellfrosvatn and tested this by using stomach content and stable isotope (δ13C and δ15N) analyses. Profundal benthic invertebrates, mainly chironomid larvae, Pisidium sp. mussels and small crustaceans, dominated the diets, and the δ13C and δ15N values indicated almost identical long-term trophic niches of the PB-morphs in both lakes. The prediction was therefore supported. This seems to indicate that the small profundal Arctic charr morphs in these lakes have evolved in parallel, in nearly identical and stable habitat and dietary niches in spite of likely different ecological interactions within the contrasting fish communities.