The biodiversity of Bathynellacea, a globally important group of groundwater crustacean, remains poorly known and understood. The objectives of this work were to increase the molecular information of bathynellaceans in order to test: 1) its usefulness solving taxonomic problems; and 2) evaluate the extent of cryptic speciation in a morphologically constrained clades from populations that have already been studied using only morphological methodology, contributing in this way to estimate the real diversity of Spanish subterranean fauna. We employ the COI barcode region to provide a preliminary assessment of the genetic subdivision, mtDNA lineages, of the genus Vejdovskybathynella, Bathynellidae, which has a restricted distribution to a karst system of Burgos (Spain) and was initially identified as a single species by morphological evaluation: Vejdovskybathynella edelweiss Camacho, 2007. We also studied the mtDNA lineages within six morphospecies of Parabathynellidae, five species belonging to Iberobathynella, a genus of wider distribution in the Iberian Peninsula, and one species belonging to the cosmopolitan genus Hexabathynella. The analyses of molecular data demonstrate the presence of highly divergent genetic units. We identify three divergent mtDNA clades, that may represent cryptic species that had gone unnoticed and possibly correspond to undescribed new species. We present a first preliminary molecular phylogeny of Bathynellacea, using three genera of Parabathynellidae and one genus of Bathynellidae, and one member of Anaspididae Thomson, 1893 as an out-group. The results of this study provide the first molecular data complementing the existing morphological knowledge to try to resolve the relations among Spanish genera and species of Bathynellacea through phylogenetic studies. Based on the results, we conclude that the evolutionary scenario of this special group of subterranean crustaceans cannot be revealed using only morphological information due to the presence of cryptic species.