The present invention provides a novel method for the recombinant production of Factor C protein from horseshoe crab using a parasitic protozoan expressing the Factor C protein. In particular, the present invention provides a parasitic protozoan host cell harboring a polynucleotide encoding horseshoe crab Factor C protein, and a method for producing Factor C protein comprising culturing said parasitic protozoan host cell under conditions such that the cells express the horseshoe crab Factor C protein. Furthermore, the present invention provides recombinant Factor C protein produced by the novel method and its use in the detection and/or removal of endotoxin.