Fish, as living organisms, are highly adaptable to natural and human-mediated environments due to their morphological, physiological and behavioural adaptations through phenotypic plasticity. In recent years, a increase of gilthead seabream in fisheries landings has been documented in the eastern Adriatic Sea, with aquaculture escapes and spillover of seabream from tuna farm concession areas contributing to population increases in natural habitats. The aim of this research was to investigate the phenotypic adaptations of gilthead seabream in a tuna farm impacted environment and to evaluate the phenotypic characteristics of wild and farmed populations in order to develop a rapid and effective tool for detecting escapes in fisheries landings. Morphological characteristics of body and otolith shape were quantified by geometric morphometrics methods, while physiological responses were studied through trophic status and sexual characteristics of protandrous populations. The year-round spatial and temporal occurrence of seabream near tuna farms indicates that they play an important role as suitable habitat for wild seabream populations in the Adriatic Sea. This altered environment, characterised by different hydrodynamics and prey availability compared to natural habitats, has triggered a specific phenotypic response of seabream by forming a new morphotype associated with tuna farms. The smaller and blunt head and the more spindle-shaped body are the main characteristics of the mentioned morphotype. In the vicinity of tuna farms, the sex change of seabream has been documented at lower lengths compared to wild populations, due to the significant trophic support that ensures better condition and reproductive status. When observing wild and farmed seabream, geometric morphometrics methods successfully assigned 99.6% of individuals to their correct origin in terms of body shape and more than 70% in terms of otolith shape. A rounder head profile with a supraterminal positioned mouth and a stocky body shape with darker and paler silver-grey coloration are the main characteristics of farmed seabream, while wild individuals are described with an elongated body and a subterminal mouth on a larger head profile. The information collected in this research can be used in future biotechnological research to identify the origin of fish through machine learning and, in the long term, in the management of escapes and the development of selection programmes for aquaculture species.