Trypanosomatids of the subfamily Strigomonadinae bear permanent intracellular bacterial symbionts acquired by the common ancestor of these flagellates. However, the cospeciation pattern inherent to such relationships was revealed to be broken upon the description of , which is sister to , but bears an endosymbiont genetically close to that of . Based on phylogenetic inferences, it was proposed that the bacterium from had been horizontally transferred to . Here, we sequenced the bacterial genomes from two isolates, including a new one from Papua New Guinea, and compared them with the published genome of the endosymbiont, revealing differences below the interspecific level. Our phylogenetic analyses confirmed that the endosymbionts of were obtained from and, in addition, demonstrated that this occurred more than once. We propose that coinfection of the same blowfly host and the phylogenetic relatedness of the trypanosomatids facilitate such transitions, whereas the drastic difference in the occurrence of the two trypanosomatid species determines the observed direction of this process. This phenomenon is analogous to organelle (mitochondrion/plastid) capture described in multicellular organisms and, thereafter, we name it endosymbiont capture.