• ecotype;
  • intraspecific diversity;
  • morphology;
  • subspecies

We compared the proportion of morphological variation accounted for by subspecies categories with the proportion encompassed by ecologically based categories in cutthroat trout (Oncorhynchus clarkii ssp.), as a means of assessing the relative importance of each approach in identifying intraspecific diversity. We used linear and geometric morphometrics to compare measures of body shape, fin length, and head features between and within subspecies of cutthroat trout. Both categories accounted for a significant proportion of the variation between and within the subspecies; however, the larger proportion was explained by subspecific differences, with the greatest morphological divergence between coastal cutthroat trout (Oncorhynchus clarkii clarkii) and interior subspecies. Ecotypic categories within each subspecies also explained significant morphological differences: stream populations had longer fins and deeper, more robust bodies than lake populations. The largest ecotypic differences occurred between stream and lake populations of Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri). Given that many cutthroat trout subspecies are of conservation concern, our study offers a better understanding of intraspecific variation existing within the species, providing precautionary evidence of incipient speciation, and a framework of describing phenotypic diversity that is correlated with ecological conditions. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 266–281.