Marine turtles are highly migratory species that establish multiple connections among distant areas, through oceanic migration corridors. To improve the knowledge on the connectivity of Atlantic green turtles Chelonia mydas, we analysed the genetic composition and contribution to juvenile aggregations of one of the world's largest rookeries at Poilao Island, Guinea-Bissau. We amplified 856 bp mitochondrial DNA (mtDNA) control region sequences of this population (n = 171) containing the similar to 490 bp haplotypes used in previous studies. Haplotype CM-A8 was dominant (99.4%), but it divided in 2 variants when the whole 856 bp was considered: CM-A8.1 (98.8%) and CM-A8.3 (0.6%). We further identified the haplotype CM-A42.1 (0.6%), found previously only in juvenile foraging grounds at Argentina, Brazil and Equatorial Guinea. The Poilao breeding population was genetically different from all others in the Atlantic (FST range: 0.016-0.961, p < 0.001). An extensive 'many-to-many' mixed-stock analysis (MSA) including 14 nesting populations (1815 samples) and 17 foraging grounds (1686 samples) supported a strong contribution of Poilao to West Africa (51%) but also to the Southwest Atlantic (36%). These findings, in particular the strong connectivity within West Africa, where illegal harvesting is still common, should motivate conservation partnerships, so that population protection can be effectively extended through all life stages. Our study expands the knowledge on migration patterns and connectivity of green turtles in the Atlantic, evidences the importance of larger sample sizes and emphasizes the need to include more finely resolved markers in MSAs and more genetic sampling from West African foraging grounds to further resolve the connectivity puzzle for this species.