A genetic linkage map of maize was constructed using 150 SSR and 24 RFLP markers, with F2 population from an elite hybrid (Zong3 x 87-1). Among 174 markers, covering whole maize 10 chromosomes, 49 markers (28.1%) showed the genetic distortion (P < 0.05). Of the total segregation distortion markers, 11 markers (22.5%) deviated toward male parent, Zong3, while 12 markers (24.5%) deviated toward female parent, 87-1, besides 25 markers (51.0%) distorted to heterozygote. Only one marker distorted to both parents. Totally, 14 segregation distortion regions (SDRs) were detected among 9 different chromosomes. Four of them were located in near regions where gametophyte genes were mapped, indicating that segregation distortion may be caused by gametophyte genes partially. Two segregation distortion regions, SDR6-1 and SDR7-1, detected in this study, seemed to be new segregation distortion regions. In this paper, reasons for segregation distortion and effects of segregation distortion on genetic mapping and QTL analysis were discussed. Regarding to QTL analysis with single locus, segregation distortion would not affect QTL mapping, but regarding to analysis of digenic interactions for epistasis, the fewer distortion markers and larger size population would be needed.