We have cloned an engrailed-class gene in the onychophoran Euperipatoides kanangrensis and investigated its expression using in situ hybridisation. The expression pattern was found to differ drastically from that previously described for another onychophoran species. In the present investigation, engrailed transcripts were detected in a subset of developing neurons in the brain anlage, and in the mesoderm as well as ectoderm of the developing limb buds. The engrailed positive cells of the brain are of differing developmental maturity, ranging from subepidermal neuronal precursors to neurons located basally in the embryo with developing axons. The lack of the traditional expression in the posterior compartment of segments reported earlier in onychophorans is discussed, and we suggest that onychophorans may have acquired two copies of engrailed with different functions. J. Exp. Zool. 304B, 2005. © 2005 Wiley-Liss, Inc.