An increasing number of invasive fruit fly pests are colonizing new grounds. With this study we aimed to uncover the invasion pathways of the oriental fruit fly, Bactrocera dorsalis into the islands of the Indian Ocean. By using genome wide SNP data and a multi-pronged approach consisting of PCA, ancestry analysis, phylogenetic inference and kinship networks, we were able to resolve two independent invasion pathways. A western invasion pathway involved stepping-stone migration of B. dorsalis from the east African coast into the Comoros, along Mayote and into Madagascar with a decreasing genetic diversity. The Mascarene islands (Reunion and Mauritius) on the other hand were colonized directly from Asia and form a distinct cluster. The low nucleotide diversity suggests that only a few genotypes invaded the Mascarenes. The presence of many long runs of homozygosity (ROH) in the introduced populations are indicative of population botlenecks, with evidence of a more severe botleneck for populations along the western migration pathway than on the Mascarene islands. More strict phytosanitary regulations are recommended in order to prevent further spread of B. dorsalis