The purpose of this study was to find out reasonable number of markers in marker-assisted selection for backcrossing breeding in soybean. The lines lacking lipoxygenases with the genetic background of Ludou 4 were used as materials; their targeted genes were detected by IEF-PAGE, and the genetic background were analyzed using SSR markers,to obtain the ideal lines for further backcross. Through the relevant analysis of genetic background recovering ratio, the appropriate marker numbers and selection method in marker-assisted selection were established. A procedure was useful in marker-assisted background selection, that is, first to use limited number of markers to screen all the individuals, eliminate the individuals not fitting the requirements, then use more makers to screen the residuals. With this method, ideal individuals can be obtained with high efficiency. Some candidate lines were chosen for further backcrossing with Ludou 4 in order to accelerate development of near-isogenic lines of Loudou 4 with different types of lipoxygenase.