The Mediterranean killifish, Aphanius fasciatus, is a euryhaline species that inhabits water bodies characterized by extreme values of salinity and temperature. All recorded localities of distribution are separated from each other due to the small number of suitable habitats, which in addition to the features of the species' biology, different pressures and threats and the absence of gene flow between populations leads local populations to extinction. The aim of this study was: describe the morphological characteristics and genetic diversity of the population in the Šćuza bay, determine the phylogenetic position and relationships in relation to other populations of this species, and to propose conservation measures for the survival of the population. Descriptive statistics was used to study the morphology, and the difference in the morphometric characteristics of males and females was investigated using the t-test. To determine relationships between populations, a phylogenetic reconstruction was used, based on cytochrome b gene sequences using the maximum parsimony, maximum likelihood and median joining. In addition, a population viability analysis determined which threats have the biggest effect on the population survival. The results place the researched population in the northern Adriatic group of Mediterranean killifish populations. Moderate genetic diversity was found, but somewhat higher than in other populations on the eastern coast of the Adriatic. Habitat degradation is recognized as the biggest threat to the survival of the population.