Molecular data inferred from three nuclear DNA regions were used to re-examine the phylogenetic position and taxonomic status of former Phoxinellus taxa. Using either distance method, maximum likelihood or MCMC, phylogenetic tree revealed statistically well supported clade of Delminichthys adspersus, Delminichthys ghetaldii, Delminichthys jadovensis, and Delminichthys krbavensis occupying a sister position to Pelasgus prespensis; furthermore, Phoxinellus pseudalepidotus emerged as a sister taxon to Delminichthys-Pelasgus group. There was a moderate support for sister relationship between Telestes croaticus and Telestes fontinalis, while the position of Telestes metohiensis varied depending on the region and method used. The topology of taxa within Delminichthys was weakly supported and remained pretty much unresoved. Our results confirm a previous notion that the former genus Phoxinellus is not a monophyletic group but rather a grouping of independent lineages.