Armeniacae Semen contains not only amygdalin but also emulsin, which is an enzyme that hydrolyzes amygdalin. This hydrolysis reaction has been a major problem associated with the water extraction of Armeniacae Semen powder. In this study, the emulsin was inactivated by extracting Armeniacae Semen powder at a constant temperature of $90^{circ}C$. In addition, in order to suppress the epimerization of D-amygdalin, the extraction time was kept to less than 8 min. The use of a 10 mM sodium phosphate buffer (pH 2.3) containing 13.5% acetonitrile as a mobile phase in reversed-phase HPLC was effective in separating and analyzing the Damygdalin and neoamygdalin. The linearity between the concentrations and detector responses was obtained in the range of 0.05 to 0.5 mM. The detection limits for D-amygdalin and neoamygdalin were approximately $5{mu}M$ per amount injected.