Using geometric morphometric methods, we evaluated the correlation between phenotypic variation and available historical and habitat information for two genetically differentiated, allopatric lineages of a widespread North American species, the brook stickleback (Culaea inconstans). Our results revealed strong patterns of structured phenotypic differentiation across the species range with extreme phenotypes occurring at the northwest and southeast range boundaries. Shape variation was broadly congruent with the distribution of two mtDNA lineages; a deep-bodied eastern form (Atlantic refugium) and a slim-bodied western form (Mississippian refugium), however, the two forms were not lineage-specific and phenotypic cladistic diversification is likely an artifact of underlying clinal variation associated with longitudinal and latitudinal gradients. In addition, we found little evidence of diagnosable lake and river forms across North America. Taken together, the results suggest that large-scale patterns of phenotypic diversity observed in C. inconstans are primarily the result of continually varying natural selection across the range and potential local gene flow, rather than historical separation or a generalized adaptive response to alternative habitats.