Histomonas meleagridis, a flagellated protozoan of the Order Trichomonadida, is the causative agent of blackhead disease in gallinaceous birds. Few genes have been identified in this organism; thus, little is known regarding the molecular basis for its metabolism, virulence, and antigenicity. To identify new genes, a cDNA library derived from a lab strain of H. meleagridis was sequenced and annotated. Data obtained from these experiments identified 3,425 H. meleagridis genes. Analysis of the data allowed the identification of 81 genes coding for putative hydrogenosomal proteins and was used to determine the codon usage frequency. Sequence information also identified bacteria that are cultured with H. meleagridis. Future analysis of these data should provide valuable molecular insights into H. meleagridis and provide the platform for molecular studies aimed at understanding the pathogenesis of blackhead disease.