<p>Marine cladocerans, primarily found in shallow coastal waters, play a crucial role in the food-web system. In Suruga Bay, Japan, cladocerans are abundant in offshore waters during the spring–summer season, dominating mesozooplankton communities. However, their roles in offshore food-webs remain unclear. This study focuses on two dominant cladoceran species in Suruga Bay, <i>Penilia avirostris</i> and <i>Pseudevadne tergestina.</i> Both stable isotope ratio and metabarcoding diet analyses were conducted to reveal their feeding habits and trophic positions in offshore food-webs. Stable isotope analysis suggested that the trophic levels of cladocerans are similar to or lower than those of other herbivorous and omnivorous zooplankton. The difference in the δ¹⁵N values between the two species indicated a lower trophic position for <i>Pe. avirostris</i> than <i>Ps. tergestina</i>. Metabarcoding analysis suggested that while the main prey organisms of the two cladocerans were similar, <i>Pe. avirostris</i> fed on small-sized prey, such as chlorophytes and cyanobacteria, unlike <i>Ps. tergestina</i>. This integrated approach suggests that <i>Pe. avirostris</i> and <i>Ps. tergestina</i> have different feeding habits and trophic positions, playing an important role in connecting lower and higher trophic levels in the offshore food-web.</p>