Abstract: Two bovine genomic DNA pools were composed of 36 high-milk-yield Chinese Holstein cattles (milk yield in 305 days>8 500kg) and 32 low-milk yield Chinese Hostein cattles (milk yield<5 600kg). 24 high polymorphic RAPD primers selected from 320 arbitrary primers were used for analyzing genetic difference between two DNA pools. 5 specific fragments were obtained from DNAs of two groups cattles. 4 of them were sequenced and converted to SCAR markers. The results of statistic analysis showed that SCAR marker yield-S139 was highly associated with milk yield trait. By electronic cloning method the marker was extended from 921 bp to 2 141 bp. As a result, the fragment was a repeat element of LINE family in bovine genome by homologous analysis. So it was reasonably to assume that some QTLs or major genes associated with milk yield trait maybe lied in this LINE region.