Bactrocera dorsalis (Hendel) is a major insect pest of commercial fruit and a quarantine priority in the European Union (EU). This tephritid species was previously recorded in Austria, France, and Italy, with more recent detections in Greece. In 2023 and 2024, B. dorsalis adult males were captured by the Federal Agency for the Safety of the Food Chain (FASFC) using traps placed in community gardens and produce markets in Belgium. Morphological identification confirmed the specimens as B. dorsalis. Genomes of trapped adults were sequenced, as well as a historical set of B. dorsalis larvae intercepted by FASFC from imported fruit. A nuclear single-nucleotide polymorphism (SNP) analysis revealed that three Belgian B. dorsalis adults originated from Africa, while eight others were of Asian origin. In contrast, almost all FASFC intercepted larvae had an African origin. A discriminant analysis of principal components (DAPC) of the “Folmer” region of the mitochondrial cytochrome c oxidase subunit I (COI) gene largely confirmed the SNP analysis but also indicated that, in a few cases, mitonuclear discordance may confound origin tracing. To enable geographic origin tracing in a laboratory setting, a diagnostic set of nuclear SNPs was developed. The DAPC was also implemented in a streamlined R-script, allowing origin assignment using a mitochondrial COI barcode. To conclude, our study reveals independent occurrences of B. dorsalis in Belgium and provides important tools for origin tracing of this quarantine pest.