The aim of this work was to evaluate the possibility of using agroindustrial residues as carbon sources for the production of omega-3 polyunsaturated fatty acids by a native Thraustochytrid strain, and analyze the microorganism growth for each substrate. In this study a Chilean strain, Thraustochytrium kinney VAL-B1, was grown in three alternative carbon sources: lupine residue, fermented wine and residual glycerol from biodiesel canola oil for biomass and polyunsaturated fatty acids production. The highest biomass production values were obtained at the fifth day of growth, which were 7.22±0.56 g L-1, 2.72±0.25 g L-1 and 6.54±0.71 g L-1 for fermentations of lupine residue, fermented wine and residual glycerol from biodiesel canola oil, respectively, while the polyunsaturated fatty acids profile showed a docosahexanoic acid percentage of 21.19%, 13.42% and 35.06% in the fermentations of the above mentioned residues. The highest omega 3 fatty acids production (docosahexanoic and eicosapentanoic acid, 2.53±0.36 g L-1 and 0.25±0.03 g L-1, respectively) was obtained in the fermentation of residual glycerol from biodiesel canola oil. With these results, it was concluded that Thraustochytrium kinney VAL-B1 produces more omega 3 fatty acids (docosahexanoic and eicosapentanoic acid) when is fermented in a medium using residual glycerol from biodiesel canola oil as an alternative carbon source, reaching a productivity of 0.50 g L-1 d-1 for docosahexanoic acid. On the other hand, the highest biomass production was obtained in fermentations of lupine residue (7.22 g L-1). For these reasons, it is feasible to employ agroindustrial by-products for polyunsaturated fatty acids production.