[2] Comparing the cranial and mandibular morphology of 23 taxa (including late archaeocetes and both fossil and extant mysticetes),[3] Bouetel & Muizon 2006 found Cetotheriidae in this traditional sense to be polyphyletic.

Based on ten cranial characters, they also concluded that of the twelve included fossil baleen-bearing mysticetes, six formed a monophyletic group, Cetotheriidae sensu stricto.

[4] Several phylogenetic studies since Bouetel & Muizon 2006 support the monophyly of a small group of core Cetotheriidae sensu stricto, archaic mysticetes with a cranium that have "a long ascending process of the maxilla with anteriorly diverging lateral border that interdigitates with the frontal" and some other characters.

[5] This group is limited to Cetotherium rathkii, Metopocetus durinasus, Mixocetus elysius, Herpetocetus scaldiensis, H. transatlanticus, H. bramblei, Nannocetus eremus, and Piscobalaena nana.

[7] Fordyce & Marx 2013 found that the pygmy right whale formed a well-supported clade with Eschrichtiidae and Balaenopteridae based on molecular data, and that, within 'cetotheres', it was most closely related to the herpetocetines (Herpetocetus and Nannocetus)[8] Bisconti et al. 2013, however, found, based on morphological data, it to be more closely related to Balaenidae (the bowhead and right whales), but added that additional specimens are expected to resolve these conflicting results within a few years.