The dispersal of organisms in an isolated environment of a hydrothermal vent remains unclear. Here, we provide direct evidence that meroplanktonic larvae may migrate thousands of meters above the ocean floor. The morphological quantitative measurements of mesozooplankton were conducted in the Onnuri Vent Field (OVF), the Solitaire Fields (SF), and the reference site (ref-site). Only one species of bivalve larva that appeared at the OVF and the ref-site (0–200 m) was similar to Bathymodiolus spp. Sixteen species of gastropod larvae were distinguished, among which, species 1–4, 6, and 13 had holoplanktonic features (Atlanta, Oxygrus, and Limacina), whereas species 5, 7–12, and 14–16 had meroplanktonic features. Species 5, 11, and 12 appeared only at the OVF, 9 and 10 appeared only in the SF, 14–16 appeared only at the ref-site, and species 7 and 8 appeared in all surveyed stations. The species 5, 8, 12, 14, and 15 have morphological features similar to Vetulonia spp., and species 7 was similar to Lepetodrilidae; species 9–11 and 16 were similar to Phymorphynchus protoconchs. The morphologically distinguished mollusk larvae in the upper layers of the water column (0–200 m) indicate that larvae associated with deep-sea hydrothermal vents may disperse approximately 2000 m above the vents.