Morphological and molecular phylogenetic data show that the Onychophora are close relatives of the Arthropoda. However, onychophoran neuromuscular junctions have been reported to employ acetylcholine, as in annelids, nematodes, and other bilaterians, rather than glutamate, as in arthropods. Here, we show that the large longitudinal muscles of Peripatoides respond indeed only to acetylcholine, whereas the oblique and ring muscles of the body wall are sensitive both to acetylcholine and to L-glutamate. Moreover, cytochemical staining reveals both acetylcholinesterase- and glutamate-positive synaptic boutons on oblique and ring muscles. These novel findings agree with a phylogenetic position of onychophorans basal to that of the arthropods. Although the glutamatergic phenotype of excitatory neuromuscular transmission may be a characteristic feature of arthropods and present even in a subset of onychophoran motor neurons, the motor neurons of the longitudinal muscles still retain the cholinergic phenotype typical for annelids and other taxa.