Sea cucumbers, one main class of Echinoderms, have a very fast and drastic metamorphosis processduring their development. However, the molecular basis under this process remains largely unknown.Here we systematically examined the gene expression profiles of Japanese common sea cucumber(Apostichopus japonicus) for the first time by RNA sequencing across 16 developmental time points fromfertilized egg to juvenile stage. Based on the weighted gene co-expression network analysis (WGCNA),we identified 21 modules. Among them, MEdarkmagenta was highly expressed and correlated with theearly metamorphosis process from late auricularia to doliolaria larva. Furthermore, gene enrichment anddifferentially expressed gene analysis identified several genes in the module that may play key roles inthe metamorphosis process. Our results not only provide a molecular basis for experimentally studyingthe development and morphological complexity of sea cucumber, but also lay a foundation for improvingits emergence rate.