East Antarctic is one of the main regions in the world that offers information of the climatic changes throughout time, due to variations of environmental conditions and forcings, that can be evidenced with long-term paleo-reconstructions methods, such as the use of biological proxies. Here we analyzed the fossil pigment composition in sediment cores from two shallow East Antarctic lakes (Mochou and Discussion) in the Larsemann Hills to reconstruct past changes in the photo-autotrophic communities in response to environmental changes and variations in the light climate. The bottom age of the sediment core from Discussion lake is 1772 cal yr BP and of Mochou Lake 30000 cal yr BP, but we restricted to the first 50 cm (ca. 9530 cal yr BP). Three different stratigraphic zones in each lake sediment core could be identified based on the fossil pigment composition. At Discussion lake, the presence of pigments between c. 1772 – 1516 cal yr BP was low, increasing in diversity c. 1516 – 288 cal yr BP, while c. 288 cal yr BP to the present there is a high concentration of carotenoids. Mochou lake c. 9530 - 6242 cal yr BP was characterized for a low concentration of pigments, from c. 6242 – 497 cal yr BP total chlorophyll and carotenoid constantly increased. The major quantity and pigment concentrations was found from c. 1895 – 497 cal yr BP. The differences in pigment composition between the lakes was confirmed by a principal component analysis (PCA) and could be tentatively linked to differences in the pigment composition of the lakes and their importance in each lake. In addition, changes in the past UVR and PAR penetration during the Middle - Late Holocene were inferred based on pigment ratios. In short, Discussion and Mochou might be influenced by environmental parameters and changes in the past climate, both lakes have a similar composition of pigments with differences in concentration, the ratios displaced periods of elevated high light penetration. We conclude that Discussion Lake presented a higher primary production and Mochou lake appear to have low productivity particularly at the early stages of the sediment core.