Aim: Food web structure plays an important role in determining ecosystem stability to perturbations. High latitude marine ecosystems are being affected by environmental stressors and ecological shifts. In the West Antarctic Peninsula these transformations are driven by climate change, and in the sub-Antarctic region by anthropogenic activities. Understanding the differences between these areas is necessary to monitor the changes that are expected to occur in the upcoming decades. Here, we compared the structure and stability of Antarctic and sub-Antarctic marine food webs. Location: Antarctic (Potter Cove, 25 de Mayo/King George Island, West Antarctic Peninsula) and sub-Antarctic (Beagle Channel, Tierra del Fuego, South America) regions. Time period: 1965 - 2019. Major taxa studied: from phytoplankton to fish. Methods: We compiled species trophic (predator-prey) interactions and calculated complexity (number of species and interactions, connectance), structure (mean trophic level, omnivory, degree distribution, modularity, species roles and traits) and stability (QSS) metrics. To be able to make statistical comparisons, we used a randomization algorithm (Strona Curveball) maintaining the number of prey and predators for each species and calculated metrics for each simulation. Results: The Beagle Channel food web presented higher values for complexity metrics (number of species and interactions), structure (mean trophic level, omnivory, modularity) but lower stability (QSS). Potter Cove fitted the exponential degree distribution, while Beagle Channel the power-law with exponential cutoff model. Both food webs presented the same connectance value (0.05), similar distribution of species in top, intermediate and top positions and topological roles, with only one network connector each. Main conclusions: Our results showed that Beagle Channel food web is more complex, but less stable and sensitive to the loss of its most connected species. While the Potter Cove food web presented less complexity and greater stability to perturbations.