In the research, the authors describe data on the study of the taxonomic diversity of microorganisms inhabiting the gastrointestinal tract, namely the ceca of domesticated pheasants of two species (Caucasian, Romanian). In addition, the isolation and identification of dominant representatives of the genus Lactobacillus as promising representatives of probiont strains was carried out. The composition of taxonomic groups of microorganisms in the contents of the ceca of pheasants was studied by a modern bacterial metagenomic research. Isolation of pure cultures of dominant species of the genus Lactobacillus from the chyme of the ceca of pheasants was carried out by classical microbiological methods. Identification of the dominant lactobacilli performed by mass spectrometry using MALDI-TOF MS. Whole-genome sequencing of the dominant members of the genus Lactobacillus was performed according to the research protocols on the MiSeq device (Illumina). The conducted bacterial metagenomic analysis revealed that in the caecal contents of the pheasants of both breeds, representatives of Proteobacteria and Firmicutes predominated at the phylum level, Gammaproteobacteria, Bacilli and Clostridia at the class level, Pseudomonadales at the order level, and Psychrobacter at the genus level. When isolating and identifying representatives of the genus Lactobacillus by mass spectrometric studies on a MALDI-TOF MS device, it was found that the dominant superiority was occupied by such species as Loigolactobacillus coryniformis, Lactobacillus johnsonii and Lactobacillus reuteri. As a result of whole-genome DNA sequencing of pure cultures of lactobacilli, their species membership was confirmed, and structures responsible for the production of a number of bacteriocins were identified in the genome of Lactobacillus coryniformis and Lactobacillus johnsonii.