Southern Hemisphere humpback whales breed in tropical waters and migrate to Antarctica to forage. While the breeding grounds are well defined, the population structure on Antarctic feeding grounds is poorly described. The Western Antarctic Peninsula (WAP) is of particular interest, where rapidly changing environmental conditions could alter prey distribution or migration pathways. To examine changes in the population of whales around the WAP, we used mitochondrial DNA (mtDNA) and 15 microsatellite loci. We compared our WAP dataset to a dataset collected 18 years earlier, and identified new haplotypes for the region, but found no significant difference between the datasets. We compared whales from the WAP to breeding populations in Oceania, Colombia, and Brazil. We used an Analysis of Molecular Variance to confirm significant genetic differentiation between the WAP and each breeding ground (overall F (ST) = 0.035/0.007 mtDNA/microsatellite, p < 0.001) except Colombia. Bayesian mixed-stock analyses showed a large apportionment to Colombia (mtDNA 93.0%; CL 91-99%; microsatellites 86%; CL 72-93%) and a small apportionment to French Polynesia/Samoan Islands (mtDNA 2.9%; CL 0.0-11.5%; microsatellites 8.9%; CL 0-22%), supporting the strong connection between Colombia and the WAP. Assignment tests allocated 81 individuals to Colombia and two to French Polynesia/Samoan Islands. No other breeding grounds had significant apportionments. Direct connectivity of French Polynesia to the WAP was confirmed with the first genotype match of French Polynesia to a feeding area. Continued genetic monitoring will highlight the complex patterns of humpbacks in this rapidly changing climate. Our results serve as a baseline for humpback whale population structure, illustrate mixed-stock analysis as a useful tool for migrating wildlife, and aid in future management considerations for humpbacks.