This dataset contains the whole genome assemblies and their annotations for seven Elopomorpha (eel, tarpon, bonefish, moray eel, Atlantic conger, ...) and one Osteglossomorpha (goldeye) species that were used to resolve the phylogenetic relationships of the early-branching teleost clades. These whole-genome analyses converged into a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (bony-tongues) as sister groups with largest lineage (clupeomorpha) as outgroup.