Brown Skua (Stercorarius antarcticus-lonnbergi) and South Polar Skua (Stercorarius maccormicki) occur throughout the Antarctic Peninsula and are sympatric in distribution over 500 km. In this region, hybridization between a male South Polar Skua and a female Brown Skua producing viable and fertile offspring. The present study aims to review the evolutionary history of South Polar Skua and Brown Skua to understand the hybridization process between these species better. To assess the evolutionary history between these species, 67 DNA samples were sequenced for AK1 locus, 70 samples for RAG1 locus, and 96 samples for Cytb locus, from individuals sampled at King George Island and Elephant Island. Cytb and RAG1 loci showed greater genetic diversity in samples from hybrid birds than those of non-hybrid individuals and may reflect the outcome of the heterosis. Overall, Brown Skua had higher genetic diversity than South Polar Skua. In addition, South Polar Skua showed probable populational expansion signals, in contrast to Brown Skua which showed population stability through time. However, our phylogenetic analysis did not corroborate the reciprocal monophyly between these species. Thus, South Polar Skua and Brown Skua show incomplete lineage sorting, indicating these species are a single taxonomic group.