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It is known that microalgae respond to different light colors, but not at single-cell level. This work aimed to assess if different light colors could be used as triggers to sort over-producing cells. Six light spectra were used: red + green + blue (RGBL), blue (BL), red (RL), green (GL), blue + red (BRL) and blue + green (BGL). Fluorescence-activated cell sorting method was used to analyse single-cell fluorescence and sort cells. BGL and RGBL lead to the highest fucoxanthin production, while RL showed the lowest. Therefore, it was hypothesized that hyper-producing cells can be isolated efficiently under the adverse condition (RL). After exposure to all light colors for 14 days, the top 1% fucoxanthin producing cells were sorted. A sorted strain from RL showed higher (16–19%) growth rate and fucoxanthin productivity. This study showed how light spectra affected single-cell fucoxanthin and lipid contents and productivities. Also, it supplied an approach to sort for high-fucoxanthin or high-lipid cells.