Many developmental genes play important roles in regeneration. Here, we cloned the two developmental genes, Wnt6 and Hox6, from Apostichopus japonicus by rapid amplification of cDNA ends (RACE) polymerase chain reaction (PCR). The Wnt6 full-length cDNA is 1140 bp long with a 1029-bp open reading frame encoding 342 amino acids. The deduced Wnt6 protein contained a 22-amino acid signal peptide and a 274-amino acid mature peptide. The Hox6 (AjHBOX6) full-length cDNA contained 1312 bp with a 966-bp open reading frame encoding 321 amino acids. Its deduced amino acid sequence included one homeodomain (60 amino acids) and three domains with low compositional complexity. Comparison and phylogenetic analysis revealed that Wnt6 and Hox6 in A. japonicus had the nearest relationship to those in sea urchins. Further expression analysis by real-time PCR showed that Wnt6 and Hox6 were apparently upregulated during intestine regeneration, which suggested that they were involved in the intestinal regeneration of sea cucumbers.