Genus Delminichthys consists of four species that live on the territory of Croatia and Bosnia and Herzegovina. Those are: spotted minnow (Delminichthys adspersus Steindachner, 1882), southern dalmatian minnow (Delminichthys ghetaldii Heckel, 1843), jadova minnow (Delminichthys jadovensis Zupančič i Bogutskaya, 2002) and krbava minnow (Delminichthys krbavensis Zupančič i Bogutskaya, 2002). The aims of this study were confirming the phylogenetic position of all species within the Delminichthys genus and the phylogenetic relationships between them, the determination of the intraspecific and intrapopulation diversity, the estimation of the effective population sizes, rates of gene flow between the populations and finally, the determination of the possible underground migratory routes between the populations of the same species. In order to analyze the phylogenetic structure of the Delminichthys genus, I used programs MEGA-X, PAUP and Network. The sequences of the control region (CR) and the mitochondrial gene for the cytochrome b (cyt b) were analyzed with the maximum parsimony (MP), maximum likelihood (ML) and median-joining (MJ) methods in order to build the phylogenetic trees and the networks that would confirm the phylogenetic structure of this genus. I confirmed the structure of four species within the genus, and with the use of the programs DnaSP and MIGRATE, I discovered that the genetic polymorphism on both intraspecific and intrapopulation levels were high, while also determining their effective population sizes as well the gene flow between their populations.