Characterisation of a sea urchin (P. lividus) homeobox gene PIHbox 9 is reported. The homeodomain of PIHbox9 is 95% identical to the homeodomain of the human HB9 gene, indicating that the two genes are highly related. Temporal expression analysis during sea urchin embryogenesis showed an absence of transcripts at early cleavage stages. At late gastrula stage, transcripts were barely detectable and reached the highest abundance at prism/early pluteus stages. By whole mount in situ hybridisation we observed a highly restricted expression in a few cells of the ectoderm-endoderm boundary of embryos at the prism stage. At pluteus stages, expression of PIHbox 9 was confined around the anus.