The present study was conducted to investigate the effects of genetic selection and threonine levels on meat quality in Pekin ducks. At 15 D of age, 192 lean ducks and 192 fatty ducks were selected and allotted to one of three treatments with 8 replicates with similar BW (8 ducks/cage), respectively. All ducks were fed the experimental diets (0.00, 0.15, and 0.30% added threonine) for 21 D from 15 to 35 D of age. The results showed that fatty ducks had higher (
P
< 0.001) feed intake, feed/gain ratio, abdominal fat percentage, and sebum percentage and lower (
P
= 0.001) breast muscle percentage compared with that of lean ducks. The fatty-type and lean-type ducks had similar weight gain and BW. Dietary threonine supplementation improved (
P
< 0.05) growth performance and increased breast muscle percentage in lean-type ducks, but it did not affect (
P
> 0.05) those indices in fatty-type ducks. Lean ducks had higher (
P
< 0.001) hepatic contents of total lipids, triglyceride, cholesterol, and plasma low-density lipoprotein cholesterol concentration, and dietary threonine supplementation decreased (
P
< 0.05) hepatic total lipid, cholesterol, and triglyceride contents in lean ducks, but it had no influence on hepatic lipids in fatty ducks (
P
> 0.05). Lean ducks had higher (
P
< 0.05) concentrations of monounsaturated fatty acid (
MUFA
), and C18-polyunsaturated fatty acid (
PUFA
) in the liver, PUFA in the breast muscle, and C18:3n6 and C18:3n3 in plasma and lower C20-PUFA and C22-PUFA in the liver and MUFA in plasma, compared with fatty ducks. Threonine supplementation increased PUFA, N3-PUFA, and n6-PUFA in plasma and hepatic fatty acids profiles in lean ducks (
P
> 0.05) but had on influence on total MUFA and total PUFA in the liver, breast muscle, and plasma in fatty ducks (
P
> 0.05). In conclusion, genetic selection toward meat production and threonine supplementation increases meat production and PUFA contents, which would influence eating quality, but it is benefit for human health.