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The production of natural omega-3 fatty acids and carotenoids through biological pathways has been gaining increased attention, especially in nutraceuticals and aquaculture industries. Recently, marine algae have been regarded as a good source for producing polyunsaturated fatty acids (PUFAs) and natural colour compounds. Algal cells vary in cell size, shape, cell walls structure and characteristics, thus it necessitates to explore various extraction methods for efficient recovery of such bioactives. Effective recovery of the colour pigments from the microbial cells is subjected to the types of extraction and combination of various methods (mechanical disruption plus chemicals) employed in the process. In this write-up, biological techniques and their combinations used for the extraction of the omega-3 fatty acids and carotenoids are discussed.