The hatching enzyme is a developmentally regulated protease secreted at the blastula stage by the sea urchin embryo to digest its protective envelope. A nearly full-length cDNA clone (HE6) encoding the entire sequence of the hatching enzyme was isolated from a prehatching blastula lambda gt11 cDNA library. The 1761 bp open reading frame codes for a preprohatching enzyme with an 18 amino acid signal sequence, a 148 amino acid activation peptide and a 421 amino acid mature enzyme which has homologies with the mammalian collagenases. Transcripts of the hatching enzyme gene are not detected in the unfertilized egg, they accumulate during the cleavage stages and disappear at hatching. This transient expression results from a transcriptional control. Thus the hatching enzyme mRNA is not a maternal gene product but a transcript synthesized at a very early stage from the zygotic genome.