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Marker transmission ratio distortion (TRD) revealed in genetic mapping studies of distant crosses can be used to infer the genetic basis relating to reproductive barriers between species.Unlike measure the degree of TRD by the overall number of segregation distorted markers in the affected genome regions,mapping the segregation distorting loci (SDL) provides reliable statistic parameters that help to confine the target genomic region for further characterization at molecular level.Using the linkage map constructed for a natural hybrid of Pinus hwangshanensis and P.massoniana,we performed SDL analyses and aligned the established map to the pine consensus map.Altogether,6 SDLs with relatively strong LOD supports were detected on 4 linkage groups of the established map.Further examination revealed that gametes inheriting different alternate chromatid blocks from the affecting genome regions had uneven chance to descend to the offspring.The corresponding chromosomal segments were supposed to play more significant role in rendering the speciation of P.hwangshanensis and P.massoniana.This paper present a case study on a crucial step for uncovering the genetic factors that triggered the uneven descending of gametes in distant crosses,and it may draw broad interest for the evolutionary biologists.