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The sub-Antarctic Magellan Ecoregion is a unique biogeographic area located at the southern tip of South America, which has exceptional marine flora and high endemism. Along the coastline, the ochrophytes Macrocystis pyrifera and Lessonia flavicans form vital underwater forests that serve as critical habitats, providing shelter, food and breeding grounds for a diverse marine organisms. These algal species are also important components used in the food industry and biomedicine, due to their high lipid, amino acid and fiber content. In this study, we investigated the intra-thallus variation of fatty acids among the different morphological structures (fronds, stipes and holdfast) of M. pyrifera and L. flavicans collected in Rinconada Bulnes during spring, 2021. The stipes of M. pyrifera (3.73 ± 1.73%) and the fronds of L. flavicans (3.35 ± 0.97%) both exhibited high lipid content. Saturated fatty acids were highest in the holdfast of M. pyrifera (37.82 ± 0.06%) followed by the fronds of L. flavicans (34.30 ± 0.10%). Notably, monounsaturated fatty acids showed higher levels en the holdfast of L. flavicans (46.45 ± 0.19%) followed by the stipes of M. pyrifera (43.04 ± 0.08%). The fronds of both M. pyrifera (32.38 ± 0.26%) and L. flavicans (28.89 ± 0.23%) showed high levels of polyunsaturated fatty acids. These findings provide valuable insight into the intra-thallus variation of fatty acids in different morphological structures of M. pyrifera and L. flavicans, highlighting their potential nutritional and biomedical importance as the most representative kelps in the Magellan region. [ABSTRACT FROM AUTHOR]