Arctic and sub-Arctic ecosystems are rapidly changing, but morphological diversity can increase a species’ resilience to these environmental fluctuations. Capelin Mallotus villosus is a cold-water forage fish distributed throughout the northern hemisphere, but is not thoroughly studied outside the Atlantic Ocean, which impedes our ability to infer the functional significance of morphometric variation among populations. The objective of this study was to use relative warps, a comprehensive geometric morphometric method, to determine if capelin populations could be distinguished by beach spawning location in the western Canadian Arctic (one location), Newfoundland, Canada (three locations), and Alaska, USA (two locations). Morphometry was examined separately by sex and compared among and within geographic regions using relative warp analysis (RWA), Procrustes ANOVA, estimates of morphological disparity, and canonical variates analysis (CVA). For both sexes, capelin from the western Canadian Arctic were differentiated from other regions, primarily by pelvic fin location. Within Newfoundland, capelin from Witless Bay, Bellevue Beach (males only), and Middle Cove were only distinguishable from each other using CVA. Within Alaska, males from Norton Sound were distinct from Prince William Sound using RWA and CVA. When all subregions were examined together, evidence for population separation was weaker for both sexes than when regions or subregions were examined separately. These morphological variations imply diversity throughout this species’ geographic distribution. Biological attributes (e.g., total length, weight, fecundity), which are influenced by multiple environmental factors such as prey availability, also varied among and within regions and may explain some of the identified morphometric diversity.