Capelin (Mallotus villosus) is an important, highly migratory marine forage fish in many northernmarine ecosystems. During 2009, spawning capelin were collected from beach and nearby deeper water(15–40 m) spawning habitats in two regions of Newfoundland ∼200 km apart (Bellevue, Trinity Bay;Lumsden, Notre Dame Bay). We used otolith chemistry to investigate connectivity by testing if age-specific chemical signatures differed between fish from different regions or spawning habitats. Traceelement concentrations (strontium, barium) did not differ between regions but did between spawninghabitats. Otolith strontium and barium during the larval period (i.e. pre-metamorphosis) resulted in suc-cessfully classifying fish spawning in each habitat (71–77%). This suggests that beach and deep-waterspawning fish experienced different environmental conditions during the larval period and, thus, pos-sibly represent different behavioral types or contingents within the broader capelin population. Thesefindings are in contrast to previous studies showing a lack of population structuring between beachand deep-water spawning fish using life history, morphometric and molecular markers (i.e. microsatel-lites). Fisheries management should aim to maintain this intraspecific complexity to buffer against futureclimate change and shifting fishing practices.