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Abstract Background Wolbachia ( w Bm) is an obligate endosymbiotic bacterium of Brugia malayi , a parasitic filarial nematode of humans and one of the causative agents of lymphatic filariasis. There is a pressing need for new drugs against filarial parasites, such as B. malayi . As w Bm is required for B. malayi development and fertility, targeting w Bm is a promising approach. However, the lifecycle of neither B. malayi nor w Bm can be maintained in vitro . To facilitate selection of potential drug targets we computationally ranked the w Bm genome based on confidence that a particular gene is essential for the survival of the bacterium. Results w Bm protein sequences were aligned using BLAST to the Database of Essential Genes (DEG) version 5.2, a collection of 5,260 experimentally identified essential genes in 15 bacterial strains. A confidence score, the Multiple Hit Score (MHS), was developed to predict each w Bm gene's essentiality based on the top alignments to essential genes in each bacterial strain. This method was validated using a jackknife methodology to test the ability to recover known essential genes in a control genome. A second estimation of essentiality, the Gene Conservation Score (GCS), was calculated on the basis of phyletic conservation of genes across Wolbachia's parent order Rickettsiales . Clusters of orthologous genes were predicted within the 27 currently available complete genomes. Druggability of w Bm proteins was predicted by alignment to a database of protein targets of known compounds. Conclusion Ranking w Bm genes by either MHS or GCS predicts and prioritizes potentially essential genes. Comparison of the MHS to GCS produces quadrants representing four types of predictions: those with high confidence of essentiality by both methods (245 genes), those highly conserved across Rickettsiales (299 genes), those similar to distant essential genes (8 genes), and those with low confidence of essentiality (253 genes). These data facilitate selection of w Bm genes for entry into drug design pipelines.