Background: Little is known about variation in catch per unit of effort (CPUE) in stickleback fisheries, or the factors explaining this variation. We investigated how nine-spined stickleback (Pungitius pungitius) CPUE was influenced by trap model by comparing the CPUEs of two very similar minnow trap models fished side-by-side in a paired experimental design. Results: The galvanized trap type (mean CPUE = 1.31 fish h–1) out-fished the black trap type (mean CPUE = 0.20 fish h–1) consistently, and yielded on average 81% more fish. Conclusions: The results demonstrate that small differences in trap appearance can have large impacts on CPUE. This has implications for studies designed to investigate abundance and occurrence of fish using minnow traps.