In July 2004 and 2006, tributaries of the River Neretva and surrounding karstic fields (polje) in Bosnia and Herzegovina were sampled, and new data on spined loaches (Cobitis) and accompanying freshwater fish fauna gathered. spined loaches were found in the River Bregava and Hutovo blato wetland, which are directly connected to the River Neretva, in the River Trebišnjica in Popovo polje, in Lake Krenica and the River Matica in Imotsko polje, and in the River Lištica drainage in Mostarsko blato. However, Cobitis were not found in karstic fields situated more westward (Livanjsko polje, Duvanjsko p., Kupreško p. and Glamočko p.), nor in karstic fields situated northward from the River Trebišnjica (Nevesinjsko polje, Fatničko p., Dabarsko p. and Gatačko p.). Neither were they found in the River Trebižat, which lies closer to the River Neretva than does Imotsko polje. Based on morphological and molecular characters, spined loaches inhabiting the rivers Trebišnjica and Bregava, and Hutovo blato were identified as Cobitis narentana Karaman, 1928, while specimens from Imotsko polje and Mostarsko blato were classified as Cobitis sp. Until now, a single species of spined loach, C. narentana, had been recorded from the lowermost part of the River Neretva basin. Our new findings suggest that the species diversity of the spined loaches in the Neretva basin in Bosnia and Herzegovina might be underestimated and that a detailed taxonomic study is required to determine the Cobitis diversity in this area.