Inter-familial relationships of the phylum Annelida have been widely studied using molecular phylogenetic/genomic approaches; however, intra-familial relationships remain scarcely investigated in most annelid families. The Maldanidae (bamboo worms) comprise more than 280 species of 40 genera and six subfamilies that occur in various environments from intertidal to hadal zones. Within this family, the taxon Maldanoplaca, which consists of four subfamilies (Maldaninae, Notoproctinae, Nicomachinae, and Euclymeninae), was proposed based on the presence of cephalic and anal plates. Phylogenetic relationships within the family remain largely undetermined based on molecular data. In this study, we reconstructed a molecular phylogeny using 52 maldanid species from six subfamilies based on two nuclear genes (18S rDNA and 28S rDNA) and two mitochondrial genes (16S rDNA and COI). Our analysis confirmed the monophyly of the subfamilies Rhodininae, Maldaninae, Lumbriclymeninae, and Nicomachinae, but neither Maldanoplaca nor the subfamily Euclymeninae were recovered as monophyletic. Nicomachinae was clustered within Euclymeninae. Ancestral state reconstruction suggested that cephalic plates were lost at least three times, despite the functional importance of capping tubes, and that anal plates were lost once. Mapping habitat depth on the phylogenetic tree suggested that habitat shifts among depth zones frequently occurred in distinct maldanid lineages.