The evolutionary history of the lower balanomorphan barnacle has remained controversial because of the complexities in shell wall ontogeny and the prevalence of plesiomorphic characteristics. Catophragmus Sowerby, 1826, Eochionelasmus Yamaguchi, 1990, Pachylasma Darwin, 1854 and Waikalasma Buckeridge, 1983 have been proposed as potentially the most primitive extant balanomorphans. In this study, we present the first molecular phylogenetic hypothesis on the evolution of lower Balanomorpha Pilsbry, 1916, based on 89 species and six molecular markers (mitochondrial 12S and 16S, nuclear 18S rRNA, histone 3, elongation factor 1a subunit and RNA polymerase subunit II). Chionelasmatoidea Buckeridge, 1983, Chthamaloidea Darwin, 1854 and Pachylasmatoidea Utinomi, 1968 intermingled, thus forming the earliest diverged lineage within the monophyletic Balanomorpha in the inferred phylogeny. Five major lineages (corresponding closely to Catophragmidae Utinomi, 1968, Chionelasmatidae Buckeridge, 1983, Chthamalidae Darwin, 1854, Pachylasmatidae Utinomi, 1968 and Waikalasmatidae Ross & Newman, 2001) were identified from this lower clade; however, the phylogenetic relationships amongst the five lineages could not be resolved in the present study. Pseudoctomeris Poltarukha, 1996 was previously considered Chthamalidae because it is a shallow-water inhabitant. However, it is nested within Pachylasmatidae in the phylogenetic analysis of the present study, and its opercular plates and rostrum are highly similar to those of Pachylasma. Bathylasmatidae Newman & Ross, 1971 and Tetraclitidae Gruvel, 1903 are sister families, whereas Austrobalanus Pilsbry, 1916 is highly diverged from the Bathylasmatidae and Tetraclitidae, supporting Buckeridge & Newman's (2010, in A review of the subfamily Elminiinae (Cirripedia: Thoracica: Austrobalanidae) including a new genus, Protelminius nov., from the Oligecene of New Zealand. Zootaxa 2349: 39-54.) proposal of full family ranking for Austrobalanidae Newman & Ross, 1976. However, Austrominius Buckeridge, 1983 and Epopella Ross, 1970 inclusions in Austrobalanidae are not supported because they are more closely related to Balanoidea and Tetraclitidae, respectively. On the basis of the molecular phylogenetic analyses in the present study and morphological evidence from previous analyses, a revised family-level classification in Pachylasmatoidea and Tetraclitoidea is proposed. [ABSTRACT FROM AUTHOR]