Scomber colias is an ecologically and economically valuable species, which is targeted by industrial and artisanal fisheries throughout its geographical distribution. Some 1,169 fish were collected by trawl onboard the R.V. “Dr. Fridtjof Nansen” in the coastal waters stretching from Morocco (~28°N) to Namibia (~22°S) and genotyped at a suite of 8 microsatellite loci. None of the statistical procedures utilized managed to detect any significant population structure. Likewise, no marker was depicted to deviate from neutral expectations. Information is available at https://imr.brage.unit.no/imr-xmlui/handle/11250/3072605 and provided in excel file called Scomber colias_microsatellite raw data.xlx, which contains three spreadsheets: 1. Geographic coordinates for each of the sampling sites that were merged into larger samples for genetic analysis. 2. Raw data for microsatellite genotypes 3. Microsatellites data in GenAlEx format ready for exportation in different file formats.