Marine associated oribatid mites belong mainly to the Ameronothroidea which represent a very small percentage of all Oribatida. Over the last decades the systematics and evolutionary history of this group has been discussed controversially and still there is no consensus concerning several issues. The extreme marine environment may have resulted in parallel morphologies complicating the classification and estimation of phylogeny based on discrete morphological traits. In the present study, we performed a molecular genetic study using a mitochondrial and two nuclear markers to infer the phylogeny of this group. Additionally, we reconstructed the phylogeny of Ameronothroidea based on morphological data using different algorithms. Both methods resulted in largely congruent topologies and highlight the following important points: the Ameronothroidea represent a paraphyletic assemblage; the Podacaridae are a distinct family and should be excluded from Ameronothridae; the Fortuyniidae, Selenoribatidae and Tegeocranellidae constitute a monophyletic lineage; and certain genera of Selenoribatidae need a revision. These results demonstrate that the classification of Ameronothroidea and certain positions within this group need to be thoroughly reconsidered and revised. The present study also shows that phylogenetic estimates based on coded morphological data can be a very helpful tool for verifying and supporting molecular phylogenies.