Pelagic fish are not generally thought to benefit from marine protected areas (MPAs) because they are highly migratory; their large home range is well beyond the usual scale of MPA boundaries. However, fishing effort for pelagic fish is often highly concentrated within the coastal zone, indicating that pelagic fish habitat in coastal regions may be predictable, and that pelagic stocks may benefit from MPAs sited in these areas. We use a novel mid-water baited video technique and otolith microchemistry to investigate the use of a coastal Australian MPA by yellowtail scad (Trachurus novaezelandiae) – the most common, and most commonly fished, small pelagic in Australian waters. Mid-water baited video sampling, combined with in-situ measurements of water properties, showed that yellowtail scad favor rocky reef areas where upwelling has occurred. Otolith microchemistry (Ba, Sr, Li, Mg, Na) showed evidence for two separate populations of yellowtail scad within the MPA: a slow-growing population that remained resident in the inner region of the MPA over our two year sample period, and a faster growing population in the outer bay. New data on pelagic fish meta-population structure, home range size and habitat preferences can be used to ensure that MPAs protect resident populations across their home range and protect migratory populations in areas where their habitat is predictable.