The aim of our research was to investigate the genetic diversity of the centipede family Lithobiidae found in Slovenian caves. The focus of our study was the species complex Lithobius stygius that we defined as the species L. stygius, its synonyms and presumably closest surface relative, L. schuleri. We acquired sequences of genetic markers COI, 16S rRNA and 28S rRNA from 184 specimens. Phylogenetic trees were computed based on COI and joined sequences, with maximum likelihood and the Bayesian method. Results show that at least 12 different centipede species are found in Slovenian caves. The complex L. stygius is, according to phylogenetic analysis, composed of four monophyletic groups: (i) L. stygius s. str., (ii) closest surface relative of the species L. stygius s. str., an undescribed species from mount Snežnik, (iii) an undescribed group of troglomophic populations, (iv) L. schuleri that is not closely related to L. stygius s. str. According to delimitation algorithms ABGD and mPTP, the species L. stygius s. str. is composed of four or seven MOTU (molecular operational taxonomic unit). Insight in phylogenetic relationships of centipedes found in Slovenian caves opens many unsolved questions and as such represents the basis of future researches on centipede diversity.