In the northeastern Pacific Ocean, there are three “ecotypes” of killer whales that differ in diet, ecology, behavior, acoustics, genetics, and morphology. Previous attempts to describe the morphological differences among populations of killer whales (Orcinus orca) have been limited to descriptive accounts or categorical studies. We used elliptical Fourier analysis (EFA) to quantify shape differences of dorsal fins and pigmentation patterns among the ecotypes from photo‐identification data of more than 500 individuals. Variation in shapes of the dorsal fin, saddle patch, and eye patch were successfully quantified using EFA, and there were highly significant (P < 0.01) differences among the ecotypes in all three morphological traits. The ability of EFA to discriminate ecotypes based on dorsal fin and eye patch shapes was substantial, while it did not perform as well for saddle patches. Visualization of the shape variation along principal component axes mirrored previous descriptions of the differences among ecotypes. Although the degree of inheritance of morphology in killer whales has not been determined, these results are consistent with previous inference of reduced gene flow between the ecotypes, and introduces elliptical Fourier analysis to the study of cetacean morphometrics.