<p>Hemichordates have occupied a central role in hypotheses of deuterostome and early chordate evolution. However, surprisingly little is understood about evolution within hemichordates, including hemichordate ancestral characters that may relate to other deuterostome taxa. Previous phylogenetic studies suggested that enteropneust worms are either monophyletic (based on 28S rDNA) or paraphyletic (based on 18S rDNA). Here, we expand the number of hemichordate taxa used in phylogenetic analyses for 18S rDNA data and employ more quickly evolving mitochondrial gene sequences. Novel data from an undescribed deep-sea enteropneust species similar to Torquarator bullocki and a Gulf Stream tornaria larva suggest that these taxa are closely allied to or possibly within Ptychoderidae. Saxipendium coronatum, another deep-sea species commonly called the spaghetti worm, is shown to be a member of Harrimaniidae. Recognition of these deep-sea lineages as distinct families calls into question features used in hemichordate taxonomy. In the new analyses, enteropneusts fall into two distinct monophyletic clades, with the colonial pterobranchs sister to Harrimaniidae, similar to earlier published 18S results. These results indicate that colonial pterobranchs may have evolved from a solitary acorn worm-like hemichordate ancestor. If true, pterobranchs would be unlikely to represent the deuterostome ancestral form as has been suggested by many traditional theories of deuterostome evolution.</p>