Segregation distortion of molecular markers has been reported in a broad range of organisms. It has been detected in an interspecific BC1 Populus pedigree established by controlled crossing between clone “LM50” (Populus tomentosa) and its hybrid clone “TB01” (P. tomentosa×P. bolleana). The study with a total of 150 AFLP markers (approximately 18.9% of the total loci) exhibited significant deviation from the Mendelian ratio (1:1) (p<0.01). Twenty-five percent of the markers were mapped on the pa-rental specific genetic linkage maps of clones “LM50” and “TB01” with a pseudo-test-cross mapping strategy. Twelve linkage groups had markers with skewed segregation ratios, but the major regions were on linkage groups TLG2, TLG4 and TLG6 in the linkage map of clone “LM50”. We also analyzed the association between distorted loci and expression of complex traits with Map-maker/QTL software. A total of 16 putative QTLs affecting 12 traits were identified in the distorted regions on seven linkage groups. Therefore we could detect the distribution of skewed loci along the entire genome and identify the association between quantitative traits and segregation loci via genetic mapping in an interspecific BC1 P. tomentosa family. Furthermore, the genetic nature and pos-sible causes of these segregation distortions for differentiation between female and male parents were also discussed. Segregation distortion of molecular markers has been reported in a broad range of organisms. It has been detected in an interspecific BC1 Populus pedigree established by controlled crossing between clone “LM50” (Populus tomentosa) and its hybrid clone “TB01” (P. tomentosa × P. bolleana). The study with a total of 150 AFLP markers (approximately 18.9% of the total loci) exhibited significant deviation from the Mendelian ratio (1: 1) (p <0.01). Twenty-five percent of the markers were code were mapped on the pa-rental specific genetic linkage maps of clones “LM50” and “TB01” with a pseudo-test-cross mapping strategy. but the major regions were on linkage groups TLG2, TLG4 and TLG6 in the linkage map of clone “LM50”. We also analyzed the association between distorted loci and expression of complex traits with Map-maker / QTL software. A total of 16 putative QTLs affecting 12 traits were identified in the distorted regio Therefore, we could detect the distribution of skewed loci along the entire genome and identify the association between quantitative traits and segregation loci via genetic mapping in an interspecific BC1 P. tomentosa family. Furthermore, the genetic biology and pos-sible causes of these segregation distortions for differentiation between female and male parents were also discussed.