Finding a new path of indirect interaction helps understand mechanisms creating natural variation of organisms’ abundance. Past studies demonstrate that in size-dependent predator-prey system, size variations in a predator species lead to density- and trait-mediated indirect interactions that have significant impacts on population and community dynamics. However, we still lack the knowledge about what type of indirect interaction arises from size variations in a prey species and how it affects on the strength of predator-prey interaction. We conducted an experiment using size-dependent predator-prey system to examine how large and small frog tadpoles (Rana pirica) affect each other’s mortality through potential predator species (Hynobius retardatus, salamander larva). This is the first empirical evidence of the negative indirect interactions between size groups within a prey species via change in shared predator’s trait (i.e. trait-mediated apparent competition).