Pelvic spine polymorphism occurs in several species in the stickleback family (Gasterosteidae). Given parallel selection driving similar phenotypic polymorphisms in multiple stickleback species, we sought to determine the extent of parallelism in the ecological consequences of pelvic spine reduction. Based on a metabarcoding analysis of brook stickleback gut contents in two polymorphic populations, we found a shift towards a planktonic diet was associated with pelvic spine reduction. These results contrast with those found in threespine stickleback where pelvic spine reduction is associated with a shift towards a benthic diet. Hence, we found non-parallel consequences of spine polymorphism across species. Furthermore, a change in gill raker morphology has been consistently implicated in the change in diet in pelvic-reduced threespine stickleback. But we found no evidence of any difference in gill raker morphology associated with pelvic spine polymorphism in brook stickleback.