The introduction of non-native species poses a threat to the structure of the endemic and native fish populations of the Prespa lakes, on the border of Greece, Albania and FYROM. Long-term monitoring has shown, for example, that the Prussian carp (Carassius gibelio) may have contributed to the reduction of water transparency (clarity), threatening the water quality of the lakes. Similarly, populations of the invasive pumpkinseed fish (Lepomis gibbossus) and the Asian topmouth gudgeon (Pseudorasbora parva) have increased in the last few years and may be related to the decreasing populations of the endemic Prespa spirlin (Alburnoides bipunctatus prespensis). It is widely accepted that the stocking of non-native fish species results in the population reduction or complete extinction of endemic species. Awareness-raising and the provision of relevant information to decision-makers and stakeholders are therefore essential to prevent detrimental effects on endemic fish species of fish stocking with non-native species.