This study presents the first molecular phylogenetic analysis of the Clinocerinae, challenging the traditionally accepted monophyly of this subfamily. DNA was extracted from fresh and museum specimens representing all biogeographical regions. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses were performed based on sequences from two mitochondrial genes, cytochrome c oxidase subunit I (COI) and cytochrome β, and three nuclear genes, carbomoylphosphate synthase domain of rudimentary, elongation factor-1α and isocitrate dehydrogenase. Through molecular data and morphological examination, our results reveal a division within Clinocerinae, distinguishing ‘typical’ or Clinocerinae (s.s.) from several genera, specifically Afroclinocera Sinclair, Asymphyloptera Collin and Proagomyia Collin, possibly lending support for a reclassification of these genera outside Clinocerinae. Bergenstammia Mik is proposed as a junior synonym of Phaeobalia Mik, syn. n., and the following new combinations are recognized: Phaeobalia albanica (Wagner) comb. n., Phaeobalia aurinae (Pusch & Wagner) comb. n., Phaeobalia carniolica (Horvat) comb. n., Phaeobalia frigida (Vaillant) comb. n., Phaeobalia glacialis (Palaczyk & Słowińska) comb. n., Phaeobalia multiseta (Strobl) comb. n., Phaeobalia nudimana (Vaillant) comb. n., Phaeobalia nudipes (Loew) comb. n., Phaeobalia pulla (Vaillant & Wagner) comb. n., Phaeobalia pyrenaica (Vaillant & Vinçon) comb. n., Phaeobalia slovaca (Wagner) comb. n. and Phaeobalia thomasi (Vaillant & Vinçon) comb. n. Re-evaluation of the genus Roederiodes resulted in the following new combinations: Clinocerella macedonicus (Wagner & Horvat) comb. n. and Clinocerella montenegrinus (Wagner & Horvat) comb. n. The origins of Clinocerinae (s.s.) are traced back to the Holarctic region, Laurasian origin, with a likely complex history of dispersal events into the Southern Hemisphere. Based on current knowledge, the greatest generic and species richness is confined to the Palaearctic Region. These findings provide valuable insights into the evolutionary relationships and distribution patterns of Clinocerinae (s.s.), challenging existing taxonomic classifications and shedding light on their historical biogeography.