Two dead birds from a flock of domestic canaries (Serinus canaria) were referred with a history of anorexia, weight loss, abdominal distension, and occasional mortality. A slightly enlarged liver and proventriculus were seen on the examination of the abdominal cavity. A large number of yeast resembling Macrorhabdus ornithogaster were observed on gram staining of the proventriculus mucosa. Pseudomonas aeruginosa was isolated on the microbial culture of the liver. The complete genomic sequence of the internal transcribed spacer 1 (ITS1) was determined in Macrorhabdus ornithogaster using panfungal primers. The alignment of the sequence obtained from this study with 6 GenBank deposited ITS1sequences of Macrorhabdus ornithogaster showed some repeated nucleotide substitutions. The complete ITS1 sequence of our study (MF993119) displayed a whole genetic similarity to ITS1 sequences of Macrorhabdus ornithogaster isolated from canaries and finches and clustered into a different group from ITS1 sequences of Macrorhabdus ornithogaster isolated from pssitacines. The ITS1 region is proposed as taxonomically informative for Macrorhabdus ornithogaster isolates from different hosts.