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.