Macrorhabdus ornithogaster, often referred to as 'megabacterium', is an ascomycetous yeast usually found colonizing the mucosal surface of the isthmus existing between the glandular and grinding stomach of a wide diversity of bird species. However, this yeast can also behave as an avian pathogen, therefore representing a potential threat to bird breeding. The aim of this work was to assess the prevalence and patterns of fecal shedding of M. ornithogaster in a colony of healthy canary birds (Serinus canaria) bred in captivity. Fresh fecal samples from 39 canaries (17 males and 22 females) were cultured in liquid media for M. ornithogaster enrichment. Only two clinically healthy females were fecal culture-positive for the yeast, which represents an overall prevalence of 5.13% in the sampled population. A close surveillance of the two culture-positive canaries, which included periodical microscopic examination of fresh stool samples, showed prolonged fecal shedding of M. ornithogaster. Nevertheless, both animals remained asymptomatic throughout the study period. To the best of our knowledge, this is the first study reporting the continuous shedding of M. ornithogaster by clinically healthy canaries.