The genus Aulopyge, represented by a single species, the Dalmatian barbelgudgeon, Aulopyge huegelii, is an endemic genus with very restricted distribution range comprising several rivers in southern Croatia and Bosnia and Herzegovina. In this study, molecular genetic analyses based on three molecular markers (one nuclear and two mitochondrial) were performed to confirm the position of Aulopyge within Cyprinidae, obtain data on its evolutionary history, and describe its population genetic structure and diversity. Specimens of A. huegelii were obtained throughout the distribution range. Phylogenetic reconstruction corroborated the independent position of this species and its placement within the Barbinae subfamily. The evolutionary history of A. huegelii started already in the middle Oligocene, whereas intraspecific divergences that left a trace in its current genetic structure and diversity are of much younger origin, starting in the middle Pleistocene. Unlike in other cypriniform species and genera distributed in the Dinaric karst region, there is no significant structuring within A. huegelii, or distribution of haplotypes concordant with the geographic scale. Furthermore, low effective population sizes estimated for most populations and low genetic diversities within them raise strong concerns about the viability and future survival of this endemic species.

The Bednja River is the longest river flowing with its full course exclusively through Croatia and one of the largest right tributaries of the Drava River, which belongs to the Danube River basin. Due to the variety of habitats present within the course of the Bednja River, as well as older literature reports, it can be expected that this river harbors a high number of freshwater fish species and would likely benefit from conservation and preservation efforts. We compiled and analyzed the existing literature data on the Bednja River fish communities and performed field investigations at various localities on this river in order to describe the current structure of its freshwater fish fauna and monitor changes induced by human activities. Our results corroborate the presence of a rich and diverse fish community. Moreover, with 36 native species, the Bednja River harbors one of the richest fish communities in Croatia as well as in the Danube basin. Unfortunately, modifications of the native fish community were evident in the form of local extinctions, reductions in the population abundance of several native species and the presence of non-native species. Habitat degradation and fragmentation were identified as the most serious threats provoking negative effects on the native fish populations, followed by predatory and competitive effects of invasive species.

The Danube barbel,Barbus balcanicusis small rheophilic freshwater fish, belonging to the genusBarbuswhich includes 23 species native to Europe. In Croatian watercourses, three members of the genusBarbusare found,B. balcanicus,B. barbusandB. plebejus, each occupying a specific ecological niche. This study examined cytochromeb(cytb), a common genetic marker used to describe the structure and origin of fish populations to perform a phylogenetic reconstruction of the Danube barbel. Two methods of phylogenetic inference were used: maximum parsimony (MP) and maximum likelihood (ML), which yielded well supported trees of similar topology. The Median joining network (MJ) was generated and corroborated to show the divergence of three lineages ofBarbus balcanicuson the Balkan Peninsula: Croatian, Serbian and Macedonian lineages that separated at the beginning of the Pleistocene. Croatian lineage ofB. balcanicusshows a uniform structure with many recently diverged haplotypes, which was further supported by the star-like shape of the MJ network. Effective size estimates were obtained for populations inhabiting separate river catchments and the results imply the good reproductive potential ofBarbus balcanicusin Croatia, which is in positive correlation with the overall high genetic diversity calculated for its populations. Nevertheless, population sizes of several population seem to be reduced as a consequence of habitat degradation and fragmentation.

Determination of the ecological state of any water body is crucial for its adequate conservation and is, moreover, required by the Water Framework Directive. Employment of multimetric indices, which integrate various anthropogenic threats to water systems with the responses of different elements of fish communities, improve our understanding and allow us to monitor the ecological state of freshwater bodies. However, design of multimetric indices that describe the ecological state of water bodies based on fish communities has already proved difficult for the Mediterranean region for several reasons, including the frequent presence of species-poor and ecologically tolerant fish communities, high endemicity and a serious lack of localities with undisturbed fish communities. The development of an ecological state index for natural water bodies in Croatia based on fish as a biological element which we present in this paper was also hindered by similar obstacles, particularly due to exceptionally high endemicity present in rivers of the Adriatic watershed, the great number of distinct water types, and significant anthropogenic pressures. Nevertheless, based on comprehensive sampling of fish communities throughout Croatia and following appropriate statistical procedures, we were able to identify stressors acting on certain water bodies, as well as responses of fish communities to them, and, finally, describe the ecological state of natural water bodies throughout Croatia. We also propose measures that will most likely help in achieving improvement and/or maintenance of the ecological states of these water bodies.

Invasive fish species pose a major threat to freshwater ecosystems by outcompeting native species and altering habitat conditions, leading to biodiversity loss. The Plitvice Lakes National Park, a UNESCO World Heritage site in Croatia, harbors a unique but species-poor native fish community, including Danube trout (Salmo labrax), Italian minnow (Phoxinus lumaireul), Italian golden loach (Sabanejewia larvata), and Italian spined loach (Cobitis bilineata). However, human-introduced species such as rainbow trout (Oncorhynchus mykiss), rudd (Scardinius erythrophthalmus), chub (Squalius cephalus), and northern pike (Esox lucius) have established thriving populations, with rudd emerging as the dominant invasive species. To mitigate their ecological impact, targeted removal efforts were implemented using casting nets and electrofishing, aiming to reduce invasive populations while minimizing harm to native species. Monitoring activities, performed during the course of the removal project, revealed significant declines in invasive fish abundance, demonstrating the effectiveness of these management interventions. Rudd abundance in Prošćansko Lake decreased by 56.9% and biomass by 69.7% over three years, while rainbow trout abundance in the B-C-M system declined by 92.7%, and its distribution shrank to a single locality, indicating strong population reduction. These findings highlight the importance of implementing active conservation measures to control invasive fish populations, thereby improving the status of native fish communities and preserving ecological balance.