The polychaete worms are problematic in that molecular phylogenetic analyses carried out the last 20 years indicate that they are not a natural (monophyletic) group; rather, this clade includes the phylums Sipunculata and Echiura, as well as a small enigmatic group of worms called the beard worms (pogonophorans+vestimentiferans; about 100 species). In addition, many analyses also now suggest that Clitellata, which has long been considered the sister group to the polychaetes, is actually a derived group of worms within the polychaetes (McHugh 1997, 2005, Struck et al 2007).

Fossil polychaetes have been found dating back to the early Cambrian. They are known mostly from fossilized jaws and mineralized tubes (Brusca and Brusca 2003).