endosymbionts in two species indicates independent acquisitions and lack of prophage elements.

is a genus of obligate bacterial endosymbionts that infect a diverse range of arthropod species as well as filarial nematodes, with its single described species, , divided into several ‘supergroups’ based on multilocus sequence typing. strains in mosquitoes have been shown to inhibit the transmission of human pathogens, including malaria parasites and arboviruses. Despite their large host range, strains within the major malaria vectors of the and complexes appear at low density, established solely on PCR-based methods. Questions have been raised as to whether this represents a true endosymbiotic relationship. However, recent definitive evidence for two distinct, high-density strains of supergroup B within and has opened exciting possibilities to explore naturally occurring endosymbionts in for biocontrol strategies to block transmission. Here, we utilize genomic analyses to demonstrate that both strains have retained all key metabolic and transport pathways despite their smaller genome size, with this reduction potentially attributable to degenerated prophage regions. Even with this reduction, we confirmed the presence of cytoplasmic incompatibility (CI) factor genes within both strains, with AnD maintaining intact copies of these genes while the gene was interrupted in AnM, so functional analysis is required to determine whether AnM can induce CI. Additionally, phylogenetic analysis indicates that these strains may have been introduced into these two species via horizontal transmission events, rather than by ancestral acquisition and subsequent loss events in the species complex. These are the first genomes, to our knowledge, that enable us to study the relationship between natural strain malaria parasites and their anopheline hosts.