Abstract Bacterial endosymbionts can inhabit certain eukaryotic compartments, yet their direct associations with mitochondria have remained poorly understood. Using a multiscale volumetric electron microscopy (vEM) framework spanning whole-cell reconstructions to subnanometer-scale electron tomography, we investigated mitochondria of two phylogenetically distinct eukaryotes: the tick Ixodes ricinus and the marine protist Diplonema japonicum . We show that Midichloria mitochondrii , the maternall