This paper presents a critical assessment of the current status and geographical distribution of loaches (Cobitidae, Nemacheilidae) in Bosnia and Herzegovina. This closes a gap in research knowledge with only general distribution data currently available. In the Danube catchment four cobitid (Cobitis elongata, C. elongatoides, Misgurnus fossilis, Sabanejewia balcanica) and one nemacheilid species (Barbatula barbatula) were recorded, while the Adriatic Sea catchment hosts three spined loaches: C. narentana, C. illyrica, and C. herzegoviniensis and nemachilid B. barbatula. Cobitis elongatoides was found to be the most common and distributed throughout the northern Bosnia and Herzegovina; i.e. in the rivers Sava, Drina, Bosna, Vrbas, Una (Danube catchment). Sabanejewia balcanica was recorded in the same area but less frequently. Recent bibliographic evidence forces us to exclude C. taenia from the current checklist. On the other hand, cobitid species from the Adriatic Sea catchment are endemic with a very small distribution. Also, the extinction risk status of each taxon is mentioned following IUCN categories. This study provides geographically constrained information on the recent status of loach populations in the freshwaters of Bosnia and Herzegovina. Further data on the status and geographical distribution would improve the conservation and management of these fishes.