Resource-based intraspecific trait variation is commonly found in vertebrates and is often discrete; relating to different resource use between populations. However, continuous trait variation within a population has received less attention. A benthic fish, Pseudogobio esocinus, occurs throughout Japan, and shows continuous variation where mouth-part morphology is related to differences in diet even within the same environment, e.g., Lake Biwa. Although chironomid larvae are the primary food of this species, individuals with a smaller and narrower mouth parts also eat amphipods, a unique prey in the lake. Therefore, we hypothesized that fish with smaller and narrower mouths are adapted for feeding on amphipods. Here we conducted an aquarium experiment to test this hypothesis. The fish were simultaneously provided two types of prey, chironomid larvae buried in the bottom and amphipods moving on the bottom. We compared the frequency of attacks and number of individuals of each prey type eaten over time. We found that the smaller and narrower mouthed fish attacked and ate more amphipods than the wider mouthed fish, thus supporting our hypothesis. This study shows that prey composition can promote to maintain continuous trait variation within a population.