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The migratory behavior of wild birds contributes to the geographical spread of ticks and their microorganisms. In this study, we aimed to investigate the dispersal and co-occurrence of <i>Francisella</i> and spotted fever group <i>Rickettsia</i> (SFGR) in ticks infesting birds migrating northward in the African-Western Palaearctic region (AWPR). Birds were trapped with mist nests across the Mediterranean basin during the 2014 and 2015 spring migration. In total, 575 ticks were collected from 244 birds. We screened the ticks for the species <i>Francisella tularensis</i>, the genus <i>Francisella</i>, and SFGR by microfluidic real-time PCR. Confirmatory analyses and metagenomic sequencing were performed on tick samples that putatively tested positive for <i>F. tularensis</i> during initial screenings. <i>Hyalomma rufipes</i> was the most common tick species and had a high prevalence of <i>Francisella</i>, including co-occurrence of <i>Francisella</i> and SFGR. Metagenomic analysis of total DNA extracted from two <i>H. rufipes</i> confirmed the presence of <i>Francisella</i>, <i>Rickettsia</i>, and <i>Midichloria</i>. Average nucleotide identity and phylogenetic inference indicated the highest identity of the metagenome-assembled genomes to a <i>Francisella</i>-like endosymbiont (FLE), <i>Rickettsia aeschlimannii</i>, and <i>Midichloria mitochondrii</i>. The results of this study suggest that (i) FLE- and SFGR-containing ticks are dispersed by northbound migratory birds in the AWPR, (ii) <i>H. rufipes</i> likely is not involved in transmission of <i>F. tularensis</i> in the AWPR, and (iii) a dual endosymbiosis of FLEs and <i>Midichloria</i> may support some of the nutritional requirements of <i>H. rufipes.</i>