Emerged Salvelinus fontinalis (brook trout) and landlocked Salmo salar (Atlantic salmon) fry of 2–4 cm total length (TL) are morphologically similar. Size at emergence, parr marks, maxillary bone length, and fin ray numbers are highly similar until fry of these species exceed 4 cm TL. Emerged brook trout and landlocked Atlantic salmon fry were examined for characteristics that would permit rapid and reliable field or laboratory identification. Relative pectoral fin length ratio (PECT/TL) provides the most robust measure separating the species in this study. Landlocked Atlantic salmon fry have a significantly larger PECT/TL than brook trout fry. Emergent fry with a PECT/TL ratio greater than 0.16 were classified as landlocked Atlantic salmon while fry with a PECT/TL ratio of less than or equal to 0.16 were classified as brook trout.