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Brown trout of non-native lineages have been stocked into Croatian streams and rivers primarily to meet angler demand. The diet of brown trout in the Black Sea Basin of Croatia is poorly understood, and there are no studies examining feeding competition between the Atlantic (AT) and Danube (DA) lineages of brown trout and their hybrids (HY). The aim of this study was to examine the natural diet of brown trout of both lineages and their hybrids and to compare feeding overlap. Canonical correspondence analysis was used to investigate the relationships between feeding habits of fish from different streams and of different genetic origin. The differences in variation of the consumed prey items were analysed by canonical variate analysis, and diet overlap was assessed by the Schoener index. The results indicate that stocked brown trout (AT) adapt rapidly to new habitat and food, as revealed by the consumption of a wide range of available food items and competition for food and space by taking on the feeding behaviour of wild native conspecifics. Diet overlap was also detected between brown trout of the DA and AT lineages. This study highlights the need to implement control measures to preserve and protect the native diversity of this species.