The 16S rRNA-based hierarchical system is considered to be the backbone of prokaryote taxonomy at the genus level and above. However, in the class Actinobacteria, the topology of the 16S rRNA-based tree is highly unsteady, and relationships between several families and orders are ambiguous. Recently, phylogenomic information was claimed to provide a more comprehensive understanding of prokaryotic systematics in the genomics era. In this article, a comparative phylogenetic analysis of the class Actinobacteria was carried out using 16S rRNA gene sequences and a set of 46 ribosomal proteins (RPs). Phylogenies based on concatenated RP sequences were generally congruent with 16S rRNA phylogenies, but higher bootstrap values supported the branching orders in the former trees. RP-based trees constructed by the maximum-likelihood and neighbor-joining algorithms provided better-defined phylogenetic relationships within the Actinobacteria and clarified the relationships and positions of several orders, such as Micrococcales and Frankiales. The RP-based phylogeny approach may thus provide a sound basis for assessing the Actinobacteria.