Eggs may serve as an alternative source for DNA extraction. The quality of DNA extracted from eggshell, whole egg liquid (WEL), and germinal disc region (GDR) was compared based on the spectrophotometric, electrophoretic, PCR, and reduced-representation library sequencing (RRLS) results. Although these DNAs were all invisible on the gel and cannot be measured spectrophotometrically, the GDR DNA was superior to the eggshell and WEL DNA in PCR efficiency. After the whole genome amplification (WGA) was introduced, the yield of GDR DNA was significantly increased. The obtaining DNA had overwhelming superiority over the eggshell and WEL DNA in the ratio of captured genome and the number of called SNP. The GDR DNA extraction followed by the WGA provides a method to obtain sufficient DNA from a single egg.