Trypanosoma (Nannomonas) congolense is an important pathogenic parasite of domestic livestock in Africa. We have cloned a cDNA encoding a prepro-cysteine protease of this protozoan, the sequence of which indicates it is an early mRNA processing intermediate. Northern analysis demonstrates a life-cycle-stage specificity similar to previously described enzymatic data. The deduced amino-acid sequence shows extensive similarity to cysteine proteases of other parasitic protozoa, as well as papain and cathepsin L. As with other African trypanosomes, a poly-proline tract connects the catalytic domain with an unusual C-terminal extension.