Simple SummaryWolbachiaare obligate intracellular bacteria that occur in insects and filarial worms. Strains that infect insects have genomes that encode mobile genetic elements that are typically lost as obligate intracellular bacteria undergo genomic streamlining. These mobile elements include diverse lambda-like prophages that package an approximately 65 kb viral genome called Phage WO, which includes a unique eukaryotic association module, or EAM. The EAM encodes unusually large proteins thought to mediate interactions between the bacterium, its virus, and the host eukaryotic cell. We propose that in addition to conventional bacteriophages,Wolbachiaalso encode smaller gene transfer agents (GTAs). From two independent preparations, we recovered an identical 15.6 kb sequence that lacks an EAM. Its small size and gene composition suggest that the element is a GTA, which may participate in the horizontal transfer of random DNA from theWolbachiagenome. Although functional proof of GTA activity remains to be obtained, these data provide a useful framework for future analysis of mobile genetic elements encoded byWolbachiagenomes.AbstractWolbachiaare obligate intracellular bacteria that occur in insects and filarial worms. Strains that infect insects have genomes that encode mobile genetic elements, including diverse lambda-like prophages called Phage WO. Phage WO packages an approximately 65 kb viral genome that includes a unique eukaryotic association module, or EAM, that encodes unusually large proteins thought to mediate interactions between the bacterium, its virus, and the eukaryotic host cell. TheWolbachiasupergroup B strain,wStri from the planthopperLaodelphax striatellus, produces phage-like particles that can be recovered from persistently infected mosquito cells by ultracentrifugation. Illumina sequencing, assembly, and manual curation of DNA from two independent preparations converged on an identical 15,638 bp sequence that encoded packaging, assembly, and structural proteins. The absence of an EAM and regulatory genes defined for Phage WO from the wasp,Nasonia vitripennis,was consistent with the possibility that the 15,638 bp sequence represents an element related to a gene transfer agent (GTA), characterized by a signature head–tail region encoding structural proteins that package host chromosomal DNA. Future investigation of GTA function will be supported by the improved recovery of physical particles, electron microscopic examination of potential diversity among particles, and rigorous examination of DNA content by methods independent of sequence assembly.