Four rumen and duodenallycannulated dairy cows were fed diets with two levels of degradable protein (110 vs. 80% of requirements) and two types of carbohydrates (NDF/starch of 2.8 and 1.3) according to a 4x4 Latin square. Rumen contents were sampled at 0, 2.5 and 5h after feeding and lyophilized for DNA extraction. Ruminal abundance of bacteria, protozoa, anaerobic fungi, methanogens and ten bacterial species were determined by quantitative PCR. Ruminal levels of microorganisms with a long generation time decreased significantly after feeding. Low protein diets decreased the rumen concentration of total bacteria (-13%) and the relative abundance of P. bryantii (-37%), methanogens (-21%), anaerobic fungi (-27%) and cellulolytic bacteria such as R. albus (-39%), F. succinogenes (-21%) and B. fibrisolvens (- 28%). High starch diets led to a decrease of ruminal amount of protozoa (-28%), fungi (- 42%), methanogens (-25%), R. albus (-20%) and S. bovis (-51%) but promoted an increase of R. flavefaciens (+78%), S. ruminantium (+43%) and M. elsdenii (P = 0.05) with respect to those levels observed in high fibrous diets. A negative relationship was observed between the efficiency of N utilization by the cow and the ruminal abundance of cellulolytic bacteria, fungi, protozoa and methanogens.