The changes the of intestinal microflora composition of Beijing broiler ducks at introduction of caroteneproduced yeast Phaffia rhodozyma biomass to the diet was studied. The positive changes of 37-days ducks intestinal microflora were revealed after two weeks of yeast P. rhodozyma biomasses application in 6-day-old birds’ diet (1% of the weight of feed). It was a decrease of the E. coli total number and pathogenic staphylococci strains, the absence of Enterobacteriaceae (lac-) strains against the high number of bifidobacteria and lactobacilli. The E. coli total number reduced by 10 times at the expense of E. coli (lac±)-strains compared to 37-day birds three weeks after the experiment. The staphylococcus non-pathogenic strains number in 58-days ducks experimental group caecum contents reduced compared to 37-day birds three weeks after the experiment. Thus, the using of caroteneproduced yeast P. rhodozyma biomass in poultry diets helps to prevent violations of intestinal microflora and occurrence dysbiosis at critical periods of growth and development.