###### Abstract  
Salmonid fish have become ecological and research models of study in the field of conservation genetics and genomics. Over the last decade, brown trout have received a high level of interest in research and publications. The term _Salmo trutta_ complex is used to indicate the large number of geographic forms present in the species _Salmo trutta_. In Europe, the _S. trutta_ complex consists (based on mitochondrial DNA control region analysis) of seven major evolutionary lineages: Atlantic (AT), Mediterranean (ME), Adriatic (AD), Danubian (DA), Marmoratus (MA), Duero (DU) and Tigris (TI). In several nations, the difficulty of identifying some lineages derives from their wide phenotypic and geographic plasticity and the presence of mixed lineages (due to introgressive hybridization with domestic AT populations). In Italy, the _S. trutta_ complex populations living in the Tyrrhenian area and on the main islands (Sicily, Sardinia and Corsica) showed high genetic diversity. Currently, on the Italian Red List, the protected (near threatened) populations are the AD and ME lineages. Recent studies based on traditional (mitochondrial and nuclear markers) and NGS (next-generation sequencing) analyses have clarified some genetic differences between the populations of the Tyrrhenian region, Sicily, Sardinia and Corsica. Native populations in Sardinia belong to the AD lineage, while those living in Corsica are mainly characterized by the AD, MA and ME haplotypes. In Sicily, in the area of the Iblei mountains, an AT lineage (North African) exists. According to some authors, the term _Salmo macrostigma_ should only be used for populations in North Africa. The use of genotyping methods based on mtDNA and nuclear markers and the latest generation sequencing techniques can improve the study of populations and evolutionary lineages in areas where there are overlaps and hybridization phenomena. S 2022 11 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 2022 20222 2022 2022 2022 2022 2  
between the ancestors _S. salar_ (Atlantic salmon) and _S. trutta_ occurred approximately 9-5 MYA [4], and that between _S. marmoratus_ and _S. trutta_ occurred approximately 4 MYA. The nucleotide divergence between _S. salar_ and the _S. trutta_ complex is less than 2% [6]. However, chromosomal rearrangements [6], chromosome number (_S. trutta_: 80 vs. _S. salar_: 54-58) and the degrees of residual tetrasomy [4] differ significantly between the two species. The _S. trutta_ complex consists of more than 60 species, including several cotypes and evolutionary lineages. _S. trutta_ originated from an ancestral form in the Paicate region. [PERSON] [7] analyzed the mitochondrial DNA control region (mtDNA CR) and found that the _S. trutta_ complex consists of five main evolutionary lines, Atlantic (AT), Mediterranean (ME), Adriatic (AD), Danubian (DA) and Marmoratus (MA), which evolved independently following allopatric fragmentation. Additional evolutionary lineages have been identified in the Duero River (Duero, DU) in Spain [8] and the Dades River (DA) [9] and Tigris River (TI) [10] in Turkey. Recently, the _S. obtusirostris_ and _S. drudanus_ forms have been included in the genus _Salmo_ as distinct species [11]. The lineage AT is distributed throughout the Atlantic basin, from Morocco to Scandinavia. The ME lineage has a native range in the Mediterranean rivers of the Iberian Peninsula, southern France, Corsica, Italy and Greece. Currently, the ME lineage is present in the middle-lower reaches of many watercourses in the Alps, from the Aosta valley to Slovenia. The ME lineage was the first to separate from the AT lineage. The AD lineage is distributed along Mediterranean rivers from the southern Iberian Peninsula to Turkey and the Apennine area in Italy and Corsica. The MA lineage originates from the rivers of the Northern Adriatic basin. The DA lineage is present in rivers flowing into the Black, Caspian, D'Aral and Persian Gulf Seas. In some areas, the AD and ME lineages show overlaps.