The method of the use of the HD 1200-E automatic amino acid analyzer for the separation of amino acids was modified for the determination of 2-6-diaminopimelic acid (DAPA) as a bacterial marker, besides the other amino acids in the acid hydrolyzates of samples of bacteria isolated from the rumen of sheep. The reproducibility of the determination of DAPA in a standard amino acid mixture found in the tests corresponded with the reproducibility of the determination of the other amino acids as indicated by the manufacturer of the apparatus. The lower limit of DAPA determination sensitivity is between 2 and 5 nmol. In samples of bacteria isolated from rumen wall, from feed particles of rumen contents and from rumen fluid, different contents of nitrogen and DAPA were obtained; this is ascribed to the different proportions of bacterial species in the bacterial populations having different functions.