Most studies on the feeding ecology of larvae and juveniles of commercially important pelagic fishes have used field-based approaches. However, due to possible biases related to net sampling, it is uncertain whether the results obtained from those studies truly represent the situation of live fish in the sea. Here we investigated the feeding ecology of pelagic fishes through a laboratory experiment minimizing the biases inherent in field net sampling. In the experiment, hatchery-reared juvenile chub mackerel (Scomber japonicus) and larval/juvenile Japanese anchovy (Engraulis japonicus) were fed with wild-caught zooplankton assemblages collected from around Hakatajima Island in the Seto Inland Sea, Japan. The relationships between fish size and prey number in the gut, and the selectivity on each prey organism were determined. As a result, in both species, prey number and size increased with body size, and the fish showed strong selectivity for crustaceans including copepodites and adults of copepods. Our data has also clearly indicated that both species can selectively prey on preferred foods that are rare while avoiding non-preferred foods that are abundant. These results, which substantially accord with reports from previous field studies, will not only help field scientists make a convincing interpretation of their data, but also open the possibility of further laboratory studies on detailed mechanisms of the feeding selectivity of larval/juvenile pelagic fishes.