Three digestive enzymes in four species of closely related prickleback fishes (family Stichaeidae: Cebidichthys violaceus, Xiphister mucosus, Xiphister atropurpureus and Anoplarchus purpurescens) were analysed to assess whether diet or phylogeny played a larger role in influencing digestive enzyme activity. Cebidichthys violaceus and X. mucosus are primarily herbivorous, whereas X. atropurpureus and A. purpurescens are mainly carnivorous. The two Xiphister species are sister taxa, and A. purpurescens is in a clade adjacent to that of the three other species. Pepsin and trypsin specific activities did not differ significantly among the four species, but α‐amylase activity was significantly higher in the two Xiphister species, followed by C. violaceus, and then A. purpurescens. The wide disparity between the two carnivores, the striking similarity between the two sister taxa, and the significant difference between the two herbivores indicate that activity of α‐amylase follows a pattern influenced more by phylogeny than by diet in these fishes.