The family Moitessieriidae is poorly known, as its members, inhabiting exclusively subterranean waters, are often known only from few minute, empty shells. Molecular studies on their relationships confirmed the distinctness of this family. Their monophyly, however, remained doubtful, since the Moitessieriidae did not form a distinct clade in the phylogenetic tree based on the most commonly applied mitochondrial cytochrome oxidase subunit I (COI), and the representative of the family Cochliopidae occupied a position among the moitessieriid clades. In the present paper two new nuclear loci, namely histone H3 gene and ribosomal internal transcribed spacer ITS2, have been applied to resolve the status of the Moitessieriidae. The resulting phylogenies show the Moitessieriidae as a distinct, well supported clade, confirming thus their monophyly.