Objectives: The population of the Saguenay-Lac-St-Jean (SLSJ) region (Quebec, Canada) is known to have a relatively high prevalence of certain hereditary disorders, which can be explained by the consequences of founder effects. This study aims at providing new insights on the origins and subregional stratification of these founder effects. Methods: The genealogies of 300 individuals were reconstructed and analyzed using the BALSAC population register. Results: Inbreeding and kinship levels are higher in Lower Saguenay than in Upper Saguenay and Lac-St-Jean. The population of Lower Saguenay also distinguishes itself because of a fewer number of distinct ancestors. Conclusion: Beyond the genetic features that characterize the whole region, SLSJ also displays intraregional variability. Thus it is important to take into account the settlement patterns and the demographic history of this population for a better appraisal of its contemporary genetic structure.