Research on ecologically and economically important sea cucumbers has been focused on temperate and tropical species, leaving those from higher latitudes, such as the Canadian Arctic, understudied. This study compared the phenotypic characters of the sea cucumber <i>Cucumaria frondosa</i> sampled from populations of the Arctic (Hudson Bay, Nunavut) and Northwest Atlantic (Newfoundland). Organ indices and external and internal tissue pigmentation, and various biochemical metrics (proximate composition, lipids, fatty acids, amino acids, lipid-soluble vitamins, carotenoids) were assessed. All sea cucumbers had similar total body weights, but those from Newfoundland had heavier gonads and body walls, while the tissue pigmentation of Nunavut individuals was distinctive (more red and yellow trivium, darker brown pigmentation). Moisture and ash contents of sea cucumbers were similar between locations; however, protein and lipid contents in Nunavut samples were 12 and 50% lower, respectively. Inversely, Nunavut samples contained more ω-3 fatty acids, a greater degree of lipid desaturation, double the concentration of proline and vitamin A, and more carbohydrates and astaxanthin than Northwest Atlantic samples. Examining phenotypic variability across latitudes and longitudes, including into the Arctic highlights unique physical and biochemical features attributed to this specific environment and may support the sustainable development of sea cucumber fisheries.