Abstratct⎯The part of the River Danube basin in the Western Balkans region (11 sampled localities and 57
in total with using of published data) revealed the remarkable diversity of brown trout assessed using the Con-
trol Region (CR) of mitochondrial DNA (mtDNA) as a molecular marker. The greatest number of brown
trout populations holds brown trout of the Da1 haplotype. Particular distinct haplotypes are limited to iso-
lated brown trout stocks. There are haplotypes of Danubian (Da), and those of Atlantic (At), Adriatic (Ad)
and marmoratus (MA) lineages introduced there. Phylogenetic relationships inferred between them implicate
the plesiomorhic character of Da*Vr, Da*Dž and Da-s6 haplotypes that were resolved as ancestral clades,
with the intermediate position between clades holding haplotypes of the non-Danubian lineage and more
advanced haplotypes of the Danubian lineage. A uniform rate of evolution was found for all clades. The recent
widespread distribution and exclusivity of Da1 haplotype imply its ancestral character among advanced
Danubian haplotypes. Populations in the Sava, Drava, Una and Drina revealed an expansion, whereas those
in the Kupa and Zapadna Morava catchments revealed both stability in size and great differentiation. Gene
flow between stocks was found to be negligible.
