A comparative study was conducted on the free amino acid composition of gilthead sea bream, Sparus aurata, and perch, Perca fluviatilis. Also the effect of 21 free amino acids on sperm motility was investigated. Spermatozoa were incubated in species-specific motility-inhibiting saline solution containing the different amino acids for 48 h. Thereafter, the motility was activated and investigated using computer-assisted cell motility analysis. Twelve free amino acids, respectively, were detected in S. aurata and P. fluviatilis semen. Arginine, cysteine, glutamic acid, leucine, and methionine occurred in semen of both species. In S. aurata, arginine, glycine, hydroxyproline, lysine, and phenylalanine in concentrations of 1.25 and 2.50 mmol/l, methionine in a concentration of 2.5 mmol/l, and serine in a concentration of 1.25 mmol/l had a positive effect on the motility of spermatozoa. In P. fluviatilis, alanine, asparagine, cysteine, glycine, isoleucine, lysine, methionine, serine, threonine, and valine in concentrations of 2.50 mmol/l positively affected motility. From these data, it can be concluded that the amino acid composition and the effect on motility are species specific. Possible consequences for spermatozoa functionality are discussed.