The complete internal transcribed spacer 1 (ITS1), 5.8S rDNA and ITS2 region of the ribosomal DNA from 11 species of rhinonyssid mites (Tinaminyssus columbae, T. minisetosum, T. sartbaevi, T. bubulci, T. melloi, T. streptopelioides, Sternostoma fulicae, S. boydi, S. strandtmanni, S. turdi, Rhinonyssus tringae) were sequenced to assess the utility of this genomic region in resolving taxonomic questions in this group and to estimate phylogenetic relationships between species. Two different geographic locations of T. melloi and T. streptopelioides were analyzed to detect intraspecies variation. Our study shows that ribosomal sequences can help to discriminate between T. melloi and T. sartbaevi, which are morphologically very close and difficult to separate by classic methods. The resulting phylogenetic tree shows some differences from the current taxonomy of the family Rhinonyssidae. This study appeals for the revision of the taxonomic status of S. boydi and closely related species which parasitize aquatic birds and suggests the synonymy of S. boydi and S. strandtmanni, despite the different hosts of the two mites.