Among the most derived calanoid copepod superfamily Clausocalanoidea about half of the genera belong to the so-called “Bradfordian” families that are defined by the presence of sensory setae at the maxilla and maxilliped. Many of these “Bradfordian” taxa are insufficiently well described, because their taxonomy is complicated and phylogenetic relationships are not completely resolved. We therefore aimed to unravel their phylogenetic relationships using molecular multi-gene analyses. We conducted molecular multi-gene analysis on 26 species from 15 genera representing all seven “Bradfordian” families using five gene fragments, the nuclear ribosomal 18S, 28S and internal transcribed spacer 2 DNA, and mitochondrial cytochrome c oxidase subunit I and cytochrome b. The monophyly of “Bradfordians” as one lineage in the superfamily Clausocalanoidea was supported by Maximum Likelihood and Bayesian Inference multi-gene analyses. Except for the support of species belonging to the same genus and specimens belonging to the same species, no phylogenetic relationships among genera and families were supported. The impossibility of resolving phylogenetic relationships among “Bradfordian” genera and families may be due to the young age or fast radiation of “Bradfordians” within the mostly derived calanoid superfamily Clausocalanoidea. Therefore, mutation rates might be not sufficient to track phylogenetic relationships. Evidence on phylogenetic relationships between genera and families remain unresolved after implementing integrated morphological and molecular taxonomic approaches.