Bosnia and Herzegovina and the Republic of Croatia are known for presence of numerous endemic species and subspecies of fish, associated with two major river basins, the Danube and the Adriatic. Rivers of the Adriatic basin are significantly short and isolated, compared with the rivers of the Danube basin. Thus, a certain number of insufficiently described endemic species exist in the Lower Neretva area, where a small number of researchers studied their ecology, biology, taxonomy and correlations between them. Three fish species that have not yet been studied in this respect are Neretva chub (Squalius svallize), Neretva rudd (Scardinius plotizza) and makal dace (Squalius microlepis). The objectives of the doctoral thesis are to define the systematic positions of these endemic species and their taxonomic relationships with other cyprinid species using molecular analysis, to complement the species identification keys established by morphometric and meristic parameters, to determine diet, growth according to von Bertalanffy and condition. Meristic and morphometric characteristics of the three studied fish species are identified in detail, and several differences in relation to previous studies, which can complement the current species identification keys, are established. The maximum recorded total length (TL) of the Neretva chub body was 28 cm, the maximum TL was 30.6 cm for makal dace, while the maximum TL of Neretva ruddwas 40.4 cm. The maximum body mass value of Neretva chub was 269.3 g, of makal dace313.80 g, and of Neretva rudd 1127.70 g, and these represent the highest values recorded in the studies so far. All this indicates a positive effect of the environmental conditions of the Lower Neretva on their growth. The number of scales in lateral line of Neretva chub is 47 to 49, in makal dace 67 to 75 with sporadic occurrences of numbers 66 and 76, while the numbers of scales in lateral line of Neretva rudd ranged from 38 to 42 with sporadic occurrences of numbers 37 and 43. The study of growth has shown that all three species have exceptionally fast growth in both length and mass, and reach much larger sizes than in rare past studies. They also achieve high condition factors, and thus confirm a very positive effect of environmental conditions on the growth of fish in the Lower Neretva area. The average value of condition factor of Neretva chub was CF = 0.98 0.14, of makal dace CF =0.97 0.03, and of Neretva rudd CF = 1.37 0.23. Positive allometric growth with a high b-value of b = 3.47 was found in Neretva chub and b = 3.25 in Neretva rudd, while the value registered in makal dace was b = 3.10, which also represents a positive allometric, i.e. nearly isometric growth. Stomach analysis provided evidence that the diet of Neretva chub consisted of diverse animal component with negligible plant component, where the class Insecta was the most frequent component in the diet of Neretva chub (Trichoptera, Diptera, Hymenoptera). The dominant diet component in stomachs of makal dace from the Matica River were the groups Ephemeroptera, Plecoptera, Trichoptera, Coleoptera and Diptera through all four seasons. Stomachs of Neretva rudd from Deransko Lake were found to contain algae, detritus, unidentified vegetable and inorganic matter, and aquatic invertebrates, of which Crustacea and Insecta occur through all four seasons. Molecular genetic analysis made it possible to clearly define their systematic position. In the DNA analysis, total of 15 samples from 3 different locations were sequenced. Based on the resulting phylogenetic tree, it is evident that the Squalius species are more related to each other, while Scardinius separates as more distant from them. In addition to primary objectives, secondary objectives were also achieved, providing a detailed insight into characteristics of the habitats of these fish species: physical and chemical characteristics of study area watercourses (the Rivers Bregava, Krupa and Matica, and Deransko Lake), and their climatic, hydrographic and hydrologic characteristics. Therefore, the intended scientific contribution in the scientific determination of kinship and systematic affiliation of the endemic cyprinids of Herzegovina and their detailed biological properties is also achieved, which is of exceptional importance in the European and global ichthyological research.