A novel protease has been identified, purified and partially characterised from complete medium grown Spirulina platensis, which could be responsible for the selective proteolysis of phycobiliproteins. It is an 80 kDa homodimeric enzyme; its N-terminal sequence is not related to any known protease sequence. It hydrolyses native phycocyanins in both crude extracts and reconstructed systems with purified Allo- or C-phycocyanin. It is inactive on several native proteins, including ribulose-1,5-bisphosphate carboxylase. The two phycocyanins are degraded at different velocities since C-phycocyanin is the better substrate, in agreement with the earlier observations on the progress of the phycobilisome disassembly. Specificity for synthetic substrates and inhibitors strongly suggests its assignment to the serine-protease family. The enzyme, however, is insensitive to the commercially available protein inhibitors of trypsin-like proteases.