Because the enigmatic arthropod relatives, such as tardigrades, onychophorans, pentastomids, and pycnogonids, have features characteristic of not only both major arthropod groups but also several other animal phyla, analysis of their phylogenetic positions may provide important clues for metazoan phylogeny in general. From analyses of complete or nearly complete 18S rDNA sequences, arthropod monophyly including all the traditional arthropod relatives was well supported. For detailed analyses within arthropods without outgroup effects, we made two reduced alignments. From the analyses of these reduced data sets, arthropods were divided into two clades: one was chelicerates and myriapods, whereas the other included crustaceans plus insects, onychophorans plus pentastomids, and tardigrades. The pycnogonids were grouped closely with the chelicerates. The Cambrian fossil record supports that myriapod-chelicerate and crustacean-insect (including tardigrades, onychophorans, and pentastomids) stems arose separately from a protoarthropod (perhaps nonarthropodized animal, such as a lobopod which has noncalcified cuticles, and nonjointed legs). Thus, the acquisition of truly arthropod characters occurred independently in the two stems. In this case, nonarthropodized characters of tardigrades, onychophorans, and pentastomids are assumed to be primitive.