Allopolyploidy is common in angiosperms, but only rarely involves different genera. One hypothesized case of intergeneric allopolyploidy is Hylocereus megalanthus, a member of Cactaceae tribe Hylocereeae, a group of vine cactus species, some of which are known for their edible fruits (“pitahaya” or “dragon fruit”). This polyploid species has been interpreted as morphologically intermediate between Hylocereus and Selenicereus. Plastid and nuclear ribosomal DNA ITS sequences from all H. megalanthus individuals sampled are either identical (plastid), or form a monophyletic clade despite considerable intraindividual polymorphism (ITS). Plastid and ITS phylogenies both show H. megalanthus nested within a well-supported Hylocereus, which in turn is nested within a paraphyletic Selenicereus. The absence of more than one lineage of ITS in H. megalanthus is consistent with autopolyploidy, but could be due to inter-homoeologue concerted evolution. Numerous low-copy nuclear genes were tested for utility in these vine cacti, and two (phyC and Vatp1) were sampled from H. megalanthus and a subset of Hylocereus and Selenicereus species. In both cases, H. megalanthus haplotypes were more closely related to each other than to other Hylocereus or Selenicereus haplotypes. Thus, we found no evidence for allopolyploidy, let alone intergeneric allopolyploidy, in H. megalanthus.