Macrorhabdus ornithogaster is an ascomycetes yeast, difficult to isolate and store in laboratory, that colonize the gut of several avian species causing digestive disorders. The present study aimed to characterize the microbiota diversity of 45 fecal samples of M. ornithogaster infected and healthy canaries from different origins (breeding and areas). Samples were collected in autumn period along a three-year time. The fecal microbiota was investigated, through the application of PCR-DGGE analysis targeting the 16S and 26S rRNA genes of DNA directly extracted from feces. The PCR-DGGE targeting the 26S clearly showed the presence of M. ornithogaster. This result, with the evaluation of clinical symptoms,has allowed the classification of the canaries in 3 different groups: healthy, infected symptomatic end infected without sintoms. The similarity matrix generated through the bacteria DGGE fingerprints was used to build a PLS-DA, as a function of the canaries status. The results showed a clear separation between healthy samples and infected with or without sintoms. The bacterial DGGE profiles were very complex but clearly indicated that the presence of M. ornithogaster can affect thebacteria microbiota composition with a possible impact on the animal status. To better understand the relationships between changes in bacterial populations in infected animals we will use the highly-throughput (nextgeneration) DNA sequencing technologies (NGS) to assess the microbiota population. A qPCR protocol will be optimized to quantify M. ornithogaster population.