The aims of the present study were to characterize the possible genetic and productive performance differences associated with the maternal selected line for six generations in Japanese quail compared to the randombred line. Body weight (BW) and shank length (SL) were recorded weekly until 5 weeks of age. BW and SL at first egg, age at first egg (AFE), first egg weight (FEW), number of days needed to produce the first 10 eggs (DN10), egg weight of the tenth egg (EW10) and egg mass of the first 10 eggs (EM10) were individually recorded for each female. The level of polymorphism between and within maternal line and a randombred line was estimated using two PCR-based DNA marker techniques RAPD and ISSR. Each line represented by 3 females and 2 males. Six RAPD and six ISSR primers were employed to find out genetic variations and relationships among these genotypes. The results indicated that line significantly affected BW at 35 days and AFE favoring the maternal line. However, the two lines insignificantly differed for BW at 1, 7, 14, 21 and 28 days of age. Females had higher insignificant BW than males at all studied ages. Line significantly affected SL at 21, 28 and 35 days of age favoring the maternal line. However, the two lines insignificantly differed for SL at 1, 7, 14 days of age and AFE. Females had higher SL than males at all studied ages, except for 14 days of age (P＞0.05). Line had significant effect on AFE, maternal line attained sexual maturity at earlier age than the randombred line by 16.50 days. Maternal line had shorter DN10 (P≤0.05) by 4.10 days than the randombred line. The females of the maternal line laid insignificantly higher FEW, EW10 and EM10 than the females of the randombred line.