Molecular methods have been used for the first time to determine the phylogeny of families, genera and species within the Pennatulacea (sea pens). Variation in ND2 and mtMutS mitochondrial protein-coding genes proved adequate to resolve phylogenetic relationships among pennatulacean families. The gene mtMutS is more variable than ND2 and differentiates all genera, and many pennatulacean species. A molecular phylogeny based on a Bayesian analysis reveals that suborder Sessiliflorae is paraphyletic and Subselliflorae is polyphyletic. Many families of pennatulaceans do not represent monophyletic groups including Umbellulidae, Pteroeididae, and Kophobelemnidae. The high frequency of morphological homoplasy in pennatulaceans has led to many misinterpretations in the systematics of the group. The traditional classification scheme for pennatulaceans requires revision. © 2013 Elsevier Inc. All rights reserved.