The near threatened yellowfin tuna (Thunnus albacares) is a commercially highly valuable species that is intensely exploited in tropical oceans around the world. Its low population structure caused by a high potential for dispersal, a continuous circumtropical distribution, and large population sizes has brought classical population assessment methods to their limits of resolution.Here we used the advances of whole genome sequencing to obtain detailed insight into the global population structure and past demography of the yellowfin tuna. A newly assembled yellowfin tuna genome enabled us to map genomic reads with 9 x average coverage, revealing up to 38 M single nucleotide polymorphism that lead to the detection of clearly differentiated Atlantic and Indo-Pacific populations, and a genetically distinct group in the Arabian Sea. Demographic inference revealed a common history for the Atlantic and Indo-Pacific yellowfin tuna. In addition, we designed a minimal diagnostic SNP set allowing to trace illegally traded yellowfin tuna and enabling follow-up studies on temporal and spatial distributions.