<p>A functional trait approach in ecology focuses on understanding the relationship between the traits of organisms (e.g. morphology, behaviour, physiology) and their roles in ecosystems, with the aim of connecting these traits to ecological functions and explaining species’ interactions with their environment and other species. In this study, we first compared the ecomorphological traits of three fragmented populations of the rapidly declining Corfu killifish <i>Valencia letourneuxi</i>; then, we compared the functional traits of the Corfu killifish with those of its native sympatric species, i.e. the Thesprotian minnow <i>Pelasgus thesproticus</i> and the Epirus riffle dace <i>Telestes pleurobipunctatus</i>, and of the alien invasive Eastern mosquitofish <i>Gambusia holbrooki</i>, in sympatry with one of the killifish populations. The killifish population in sympatry with the mosquitofish differed from the two killifish populations in mosquitofish-free habitats in pectoral fin position, pectoral fin ratio and pectoral fin surface ratio, which are associated with fish position in the water column, manoeuvrability and propulsion. In addition, the riverine killifish population, in a high flow variability habitat, differed in body mass, throt and caudal fin ratio from the other two populations that occupy hydrologically stable environments, traits associated with differences in hydrodynamics. The Corfu killifish shared only one trait with the native minnow and one with the native riffle dace, indicating they occupy different ecological niches, while it shared several functional traits with the mosquitofish, which related to feeding, prey detection and swimming performance. The notable functional overlap between the Corfu killifish and the invasive mosquitofish underscores the ecological vulnerability of the killifish to mosquitofish impacts, which may lead to further decline and ultimately to its displacement.</p>