A submarine cave is a unique environment that is dark, food limited, semi-isolated from the outside, and sheltered from wave action. However, our knowledge of the long-term change in submarine-cave ecosystems remains limited. We document here the community-scale responses toward long-term change in a submarine cave, Daidokutsu in Okinawa in southern Japan. Using both metazoans (ostracods and bivalves) and protozoans (larger benthic foraminiferans) in two sediment cores obtained from the cave, we reconstruct the faunal and diversity changes of the past 7 Kyr. All taxonomic groups showed long-term, gradual linear change of faunal composition from predominantly open-water taxa to predominantly cave taxa, and ostracods showed short-term variability of species diversity. The long-term faunal trend probably reflects gradual isolation of the cave ecosystem due to coral reef development (i.e., development of the cave ceiling) during periods of the Holocene transgression and subsequent sea-level highstand. The short-term diversity changes show substantial similarity to centennial- to millennial-scale Holocene Asian monsoon variability. Ostracod species diversity peaks tend to correspond with periods of strong East Asian winter monsoons. The results indicate that limestone submarine-cave ecosystems, an important cryptic habitat, developed gradually during the Holocene and may be sensitive to rapid climate changes.