Amino acid (AA) composition of body protein is considered constant although there are evidences that AA pattern in pigs may be altered by different factors. Pigs with different body composition and protein deposition rates—like fatty and lean pigs—may differ in AA composition, with possible consequences on their AA requirements. This work investigates effects of genotype and dietary lysine deficiency on AA composition of carcass and muscles of Iberian and Landrace × Large White pigs. Twenty‐eight barrows (10 kg body weight [BW]), 14 from each breed, were used. They were randomly assigned to two experimental diets according to a factorial arrangement (two breeds × two diets). Diets were isonitrogenous and isoenergetic (200 ± 1 g CP/kg dry matter (DM); 14.7 ± 0.1 MJ ME/kg DM) and with identical chemical composition except for lysine concentration (10.9 and 5.20 g lysine/kg DM, for lysine‐adequate (AL) diet and lysine‐deficient (DL) diet respectively). Pigs were individually housed, and daily feed allowance was adjusted on a weekly basis according to BW. Pigs were slaughtered at 25 kg BW. Isoleucine, valine and phenylalanine concentration were higher in carcass protein of Iberian pigs (p < .01). In longissimus muscle, higher concentration of arginine, isoleucine, phenylalanine, lysine and valine (p < .001–p < .05), and lower of methionine (p < .001) were detected in Iberian pigs, whereas phenylalanine, leucine, lysine, threonine and methionine concentration decreased and arginine increased (p < .001–p < .05) when pigs were fed DL diet. Genotype and lysine deficiency effects were moderate in the AA composition of protein of biceps femoris muscle. The results show that AA proportions in protein of carcass and longissimus muscle can be influenced by pig genotype and conditions of lysine shortage. The biceps femoris muscle, with different functional and metabolic properties, shows more constant AA composition than longissimus, which seem to prevail independent from genotype or nutritional challenges.