Sea-level fluctuations in the marginal seas of the northwestern Pacific Ocean during the Pleistonene have profoundly influenced the genetic structure of marine organisms. Previous phylogeographic studies have mainly focused on fish and molluscs; other taxonomic groups have been poorly studied, which restricts a comprehensive understanding of the geogenetic patterns of marine species in this area. To precisely understand how environmental factors and historical events shape the population structure of the sea pen Cavernularia obesa in the East China Sea, we determined partial nucleotide sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene in 71 individuals from five sites. Results of population Genetic and demographic analyses revealed a low genetic diversity within each population. Moreover, the historical population size change showed that the populations experienced bottlenecks during the Pleistonene. The sea level of the East China Sea decreased by >100 m when the glacial advanced during the Pleistonene, which caused the shrinking of habitats for marine species and eventually resulted in low genetic diversity within the populations in this area.