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In the areas of the Russian Far East, there are two ecotypes of killer whales: fish-eating R-type and mammal-eating T-type. Although the ecotypes are partially sympatric, they are reproductively isolated even in areas where they live together. The previous studies in the same area were limited to the qualitative description of the morphological differences between the two ecotypes. In this study, we compared the shape of dorsal fins of R-type and T-type killer whales using elliptical Fourier analysis to quantify the shape differences of the dorsal fin between the killer whale ecotypes. The analysis was performed using momocs package in R. Principal component analysis of Euclidean distances between shape coordinates was performed, and principal component scores were evaluated using multivariate analysis of variance (MANOVA). The principal component scores for each shape were used as the dependent variables in the MANOVA, and ecotype was used as the grouping factor. MANOVA found significant difference (p < 0.01) between the shape of R-type and T-type dorsal fins. The analysis allowed us to quantify the level of differences in the studied morphological characteristics in the killer whale ecotypes from different regions. Statistically significant difference in the dorsal fin shape between the ecotypes confirms their long-term reproductive isolation and indicates the possibility of distinguishing them by their appearance in the field.