Habitats for pond-breeding salamanders are declining as a result of land development and management abandonment. In that context, a pond-breeding salamander Hynobius tokyoensis has recently been known to breed in small streams. However, little is known about the ecology of pond-breeding salamander larvae, such as food, in small streams. Here, to gain insight into foraging ecology of Hynobius tokyoensis larvae in small steams, we investigated the potential prey items in nine small streams running through secondary forests in Hachiouji City, Tokyo, Japan. In addition, we hypothesized that H. tokyoensis larvae preferentially predate active prey invertebrates over less-active prey because they are generalist, sit-and-wait predators. To test this hypothesis, we experimentally examined predation frequencies by H. tokyoensis larvae on the two major arthropod species (isopods and Plecoptera larvae) and activity (i.e., movement frequencies and distances) of the potential prey. As a result, isopods (Asellus hilgendorfii) and Plecoptera (Nemouridae larvae) are the two dominant aquatic invertebrates in small streams inhabited by H. tokyoensis, larval salamanders consumed more isopods than Plecoptera larvae and isopods are more active than Plecoptera larvae. Taken together, we concluded that isopods should be the main prey for salamander larvae inhabiting small streams due to their high abundance and conspicuous activities.