The degree of taxonomic congruence between three methods of classification is examined for three Quebec populations of wild brook trout, Salvelinus fontinalis, from the Matamek–Moisie watersheds. The three methods utilize morphometric, meristic, and electrophoretic characters. Electrophoretic comparison is also made between the Quebec samples and brook trout from the Dorion Hatchery, Ontario. Using discriminant function analysis on data for the three Quebec populations, a subset of nine morphometric measurements was identified with between 84.0 and 92.6% correct classification, and a meristic subset of four characters, including mandibular pores, with between 72.5 and 95.0% correct classification. Electrophoretic analysis has identified a number of newly defined alleles at four loci, from five tissues. The meristic and electrophoretic analyses show congruence in the order of similarity and, therefore, are considered the most suitable methods for classification of the brook trout. Morphometric analysis provides an insight into localized adaptation particularly in response to habitat and resource utilization. An understanding of the taxonomic status of populations of brook trout requires not only a definition of individuals in terms of meristic and electrophoretic profiles, but also morphological characterization, to increase our understanding of their ecology and response to other faunal components.