High levels of both glutamine synthetase and a unique L-glutamine- and N-acetyl-L-glutamate-dependent carbamoyl phosphate synthetase are present in the mitochondria in livers of marine urea-retaining elasmobranchs (Casey, C. A., and Anderson, P. M. (1982) J. Biol. Chem. 257, 8449-8453). On the basis of these observations it has been suggested that in these species carbamoyl phosphate and, consequently, one of the nitrogen atoms of citrulline and, ultimately, urea, are derived directly from glutamine rather than from ammonia as occurs in mammalian ureotelic species. The purpose of this study was to obtain evidence for this role of glutamine. Isolated hepatic mitochondria from Squalus acanthias incubated with ammonia plus glutamate, ornithine, bicarbonate, inorganic phosphate, and succinate as an energy source were found to synthesize citrulline at a rate comparable to the rate of urea synthesis observed in vivo. Citrulline synthesis proceeds at maximal rates even when the ammonia concentration is as low as 0.05 mM and is stoichiometric with the amount of ammonia initially present. Synthesis from ammonia does proceed in the absence of glutamate, but a much higher concentration of ammonia (congruent to 4 mM) is required to achieve a half-maximal rate. Glutamine can substitute for ammonia plus glutamate as the nitrogen-donating substrate for citrulline synthesis. Selective inhibition of the glutamine-dependent activity of the carbamoyl phosphate synthetase in the isolated mitochondria completely inhibits the ability of the mitochondria to synthesize citrulline from glutamine or from ammonia plus glutamate, whereas selective inhibition of glutamine synthetase inhibits citrulline synthesis from ammonia plus glutamate, but not from glutamine. These observations provide direct evidence that ammonia assimilation for citrulline synthesis (and, therefore, urea synthesis) in these species involves intermediate formation of glutamine.