The brown trout form the Salmo trutta complex, a diversified assemblage of salmonids. Its native area mainly covers Europe. It can develop three ecological forms or ecotypes, depending on its migratory behaviours: resident, anadromous (going to sea) and lacustrine (going to lakes). The sea trout is the anadromous ecotype, born up river, living at sea where it reaches salmon size, and returning to the river of its birth for spawning. Like other anadromous fish species, this natural ecotype is protected in France. While its distribution along the Atlantic coasts is known, the sea trout is considered absent in the Mediterranean basin. However, some isolated individuals have been observed in the Rhône River and some other rivers from southern France. In order to understand the genetic position of these large specimens swimming upstream in Mediterranean rivers, and despite the degraded DNA due to bad tissue preservation, eight samples of these trout, mainly caught by anglers, were successfully genotyped at seven microsatellite loci and three sequenced at the mitochondrial Control Region. All specimens tested belong to the Atlantic lineage and are probably stocked domestic trout. This study provides preliminary elements for the conservation status of this ecotype in the Mediterranean basin.