Abstract: The amino acid and fatty acid profiles of the breasts and thighs of Peking and Muscovy ducks were analyzed in this study. Amino acid profiles were performed in duplicate and fatty acid profiles were performed in triplicate. The chemical score, amino acid score and essential amino acid index were calculated from the amino acid profiles, whereas the SFA, MUFA, PUFA, ω3, ω6 and ω6:ω3 ratio were calculated from the fatty acid profiles. In general lysine and methionine were the highest EAA found in Pecking and Muscovy ducks, whereas their methionine contents were relatively higher than in other poultry meat. Muscovy meat possesses a higher (p<0.05) chemical and amino acid score compared to Peking duck meat. No significant difference (p>0.05) in the EAA index was observed between different body parts and different species. The concentration of the fatty acid C18:1ω9 was the highest observed in both Peking and Muscovy duck species. The SFA of Muscovy breast was significantly higher (p<0.05) than that of Peking breast. The MUFA of Muscovy was significantly higher (p<0.05) than that of Peking duck, both in breast and thigh cuts; moreover, the MUFA of Muscovy thigh was significantly higher (p<0.05) compared to that of Muscovy breast. The PUFA of Muscovy breast was significantly lower than that of Peking breast. Both Peking and Muscovy ducks meats show high protein quality and are good sources of fatty acids for human consumption.