Matrilineal phylogenetic divergence among Atlantic salmon stocks of the Bay of Fundy in south eastern Canada is investigated. Sequence variation in two regions of the mitochondrial ND1 gene, encompassing 710 base pairs, is described for 168 salmon from 11 rivers. Mean overall haplotype and nucleotide diversity (h and pi) observed are 0.5014 and 0.00095, respectively. Nested clade analysis (NCA) and molecular analysis of variance (AMOVA) both point to highly restricted gene flow among rivers and show the haplotype distribution to be geographically structured. Variation among predefined regions of the Bay (16%) is greater than among populations within these regions (14%) The main regional differentiation occurs between rivers of the geographically isolated inner Minas Basin and those elsewhere in the Bay. Differentiation most probably reflects the pattern and nature of the historical processes associated with post-glacial colonisation of the area by salmon following the last Pleistocene glacial maximum c. 180,00 yrs BP.