Recent molecular data, both from rRNA and from mtDNA as well as embryological data, strongly supports the hypothesis that living agnathans, the cyclostomes, are monophyletic.
The oldest fossil agnathans appeared in the Cambrian, and two groups still survive today: the lampreys and the hagfish, comprising about 120 species in total. Hagfish are considered members of the subphylum Vertebrata, because they secondarily lost vertebrae; before this event was inferred from molecular and developmental data, the group Craniata was created by Linnaeus (and is still sometimes used as a strictly morphological descriptor) to reference hagfish plus vertebrates.
While a few scientists still regard the living agnathans as only superficially similar, and argue that many of these similarities are probably shared basal characteristics of ancient vertebrates, recent taxonomic studies clearly place hagfish (the Myxini or Hyperotreti) with the lampreys (Hyperoartii) as being more closely related to each other than either is to the jawed fishes.
^ abcDelarbre C, Gallut C, Barriel V, Janvier P, Gachelin G (February 2002). "Complete mitochondrial DNA of the hagfish, Eptatretus burgeri: The comparative analysis of mitochondrial DNA sequences strongly supports the cyclostome monophyly". Molecular Phylogenetics and Evolution. 22 (2): 184–92. doi:10.1006/mpev.2001.1045. PMID11820840.
^Janvier, P. (November 2010). "MicroRNAs revive old views about jawless vertebrate divergence and evolution". Proceedings of the National Academy of Sciences of the United States of America. 107 (45): 19137–19138. Bibcode:2010PNAS..10719137J. doi:10.1073/pnas.1014583107. PMC2984170. PMID21041649. Although I was among the early supporters of vertebrate paraphyly, I am impressed by the evidence provided by Heimberg et al. and prepared to admit that cyclostomes are, in fact, monophyletic. The consequence is that they may tell us little, if anything, about the dawn of vertebrate evolution, except that the intuitions of 19th century zoologists were correct in assuming that these odd vertebrates (notably, hagfishes) are strongly degenerate and have lost many characters over time.