Recent advances in molecular genetics have provided hundreds of thousands of single nucleotide polymorphisms (SNPs) to detect mutations in genes related with complex traits. Undetected shared ancestry within samples of individuals could lead to the detection of false genomic signals in association mapping. Pedigree-based relationship matrices or genomic relationship matrices could be used in a mixed model to predict and correct for genetic stratifications. Genotypic information of founder populations could also be used to explore patterns of inheritance for complex traits by admixture mapping. An F 2 population was created using M16 and ICR mouse lines for studying body weight at 8 weeks of age. Genotypes were collected for 1813 SNPs for each animal, including the founders. Bayesian residuals were used for population stratification in the admixture model. Association and admixture mapping detected similar genomic signals from chromosome 10. Our results provide empirical proof that gene flow from ancestral populations could be traced by admixture mapping with founder genotypes.