OTUBAINS are a recently discovered family of cysteine proteases that participate in the ubiquitin pathway. These proteins were originally described in animal systems and are involved in removing the ubiquitin chain attached to a protein destined for degradation. In a cDNA-AFLP screen designed to identify genes that are expressed during early somatic embryogenesis in the conifer Pinus radiata, a fragment-derived transcript corresponding to an Otubain-like cysteine protease was identified. The full-length cDNA contained an 885 bp ORF encoding 294 amino acids, and was named PrOTUBAIN. The deduced protein showed high identity to other OTUBAINS and contained an OTU domain and a catalytic triad characteristic of cysteine proteases. The 3-D model of PrOTUBAIN showed significant similarity to human OTUBAIN2, suggesting that the plant protein may possess functions similar to that of the human protein. Real time PCR assays demonstrated that PrOTUBAIN is expressed in different tissues and that transcript are particularly abundant in embryogenic tissues. This is the first report of this class of protein in higher plants and the putative role of PrOTUBAIN is discussed.