Maternally transmitted Wolbachia infect about half of insect species, yet the predominant 1 mode(s) of Wolbachia acquisition remains uncertain. Species-specific associations could be old, 2 with Wolbachia and hosts co-diversifying (i.e., cladogenic acquisition), or relatively young and 3 acquired by horizontal transfer or introgression. The three Drosophila yakuba-clade hosts ((D. 4 santomea, D. yakuba), D. teissieri) diverged about three million years ago and currently 5 hybridize on Bioko and São Tomé, west African islands. Each species is polymorphic for nearly 6 identical Wolbachia that cause weak cytoplasmic incompatibility (CI)-reduced egg hatch when 7 uninfected females mate with infected males. D. yakuba-clade Wolbachia are closely related to 8 wMel, globally polymorphic in D. melanogaster. We use draft Wolbachia and mitochondrial 9 genomes to demonstrate that D. yakuba-clade phylogenies for Wolbachia and mitochondria tend 10 to follow host nuclear phylogenies. However, roughly half of D. santomea individuals, sampled 11 both inside and outside of the São Tomé hybrid zone, have introgressed D. yakuba mitochondria. 12 Both mitochondria and Wolbachia possess far more recent common ancestors than the bulk of 13 the host nuclear genomes, precluding cladogenic Wolbachia acquisition. General concordance of 14 Wolbachia and mitochondrial phylogenies suggests that horizontal transmission is rare, but 15 varying relative rates of molecular divergence complicate chronogram-based statistical tests. 16 Loci that cause CI in wMel are disrupted in D. yakuba-clade Wolbachia; but, a second set of loci 17 predicted to cause CI are located in the same WO prophage region. These alternative CI loci 18 seem to have been acquired horizontally from distantly related Wolbachia, with transfer 19 mediated by flanking Wolbachia-specific ISWpi1 transposons. 20 21 22 23 24 25 26 27 28 29clade (Lachaise et al. 2000; Bachtrog et al. 2006; Llopart et al. 2014; Turissini and Matute 2017; 92 Cooper et al. 2018), and the Wolbachia infecting all three species (wSan, wTei, and wYak) are at 93 intermediate frequencies and identical with respect to commonly used typing loci (Lachaise et al. 94 2000; Charlat et al. 2004; Cooper et al. 2017). 95 Horizontal Wolbachia transmission has been repeatedly demonstrated since its initial 96 discovery by O'Neill et al. (1992) (e.g., Baldo et al. 2008 Schuler et al. 2016), and it may be 97 common in some systems (e.g., Huigens et al. 2000; Huigens et al. 2004; Ahmed et al. 2015; Li 98 et al. 2017). Phylogenomic analyses indicate recent horizontal Wolbachia transmission, on the 99 order of 5,000-27,000 years, among relatively distantly related Drosophila species of the D. 100 melanogaster species group (Turelli et al. 2018); but there is little evidence for non-maternal 101 transmission within Drosophila species (Richardson et al. 2012; Turelli et al. 2018). Horizontal 102 Wolbachia transfer could occur via a vector (Vavre et al. 2009; Ahmed et al. 2015) and/or via 103 shared ...