The genes otd/otx, six3, pax6 and engrailed are involved in eye patterning in many animals. Here, we describe the expression pattern of the homologs to otd/otx, six3, pax6 and engrailed in the developing Euperipatoides kanangrensis embryos. Special reference is given to the expression in the protocerebral/ocular region. E. kanangrensis otd is expressed in the posterior part of the protocerebral/ocular segment before, during and after eye invagination. E. kanangrensis otd is also expressed segmentally in the developing ventral nerve cord. The E. kanangrensis six3 is located at the extreme anterior part of the protocerebral/ocular segment and not at the location of the developing eyes. Pax6 is expressed in a broad zone at the posterior part of the protocerebral/ocular segment but only weak expression can be seen at the early onset of eye invagination. In late stages of development, the expression in the eye is upregulated. Pax6 is also expressed in the invaginating hypocerebral organs, thus supporting earlier suggestions that the hypocerebral organs in onychophorans are glands. Pax6 transcripts are also present in the developing ventral nerve cord. The segment polarity gene engrailed is expressed at the dorsal side of the developing eye including only a subset of the cells of the invaginating eye vesicle. We show that engrailed is not expressed in the neuroectoderm of the protocerebral/ocular segment as in the other segments. In addition, we discuss other aspect of otd, six3 and pax6 expression that are relevant to our understanding of evolutionary changes in morphology and function in arthropods.