Hedgehog (hh) is a multifunctional extracellular protein, and known as an essential signal molecule in morphogenetic movement in animal embryos. We have cloned, sequenced, and studied dynamic localization of Hphh, a hedgehog homologue of the sea urchin, Hemicentrotus pulcherrimus. The origin of Hphh transcribing cells was also verified during early embryogenesis. The amino acid sequence of Hphh shows high homology to Lvhh, an hh homologue cloned in the sea urchin, Lytechinus variegatus. Reverse transcriptase polymerase chain reaction showed that the transcription of Hphh occurred at and after 19 h post-fertilization (19 hpf) mesenchyme blastula stage until, at least, 69 hpf 4-arm pluteus stage. Whole mount in situ hybridization showed Hphh transcription sites in a few cells at the tip of archenteron in 30 hpf gastrulae. At around 45 hpf 2-arm pluteus stage, the number of Hphh transcribed cells was 8, and unequally split to two groups, 5 cells in left coelomic sac and 3 cells in right coelomic sac. A cell lineage tracing by staining the small micromeres with 5-Bromo-2-deoxyuridine showed that Hphh was transcribed exclusively in all the small micromere descendants and comprised the coelomic sacs in 69 hpf plutei.