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The visualization of misfolded Aβ peptides by using fluorescence chemical dyes is very important in Alzheimer’s disease (AD) diagnosis. Here, we describe the fluorescent substance, fucoxanthin, which detects Aβ aggregates in the brain of AD transgenic mouse models. We found that fucoxanthin from the microalgae Phaeodactylum tricornutum has fluorescent excitation and emission wavelengths without any interference for Aβ interaction. Thus, we applied it to monitor Aβ aggregation in AD transgenic mouse models. Aβ plaques were visualized using fucoxanthin in the brain tissue of APP/PS1 and 5×FAD mice by histological staining with different staining methods. By comparing fucoxanthin-positive and thioflavin S-positive stained regions in the brains, we found that they are colocalized and that fucoxanthin can detect Aβ aggregates. Our finding suggests that fucoxanthin from P. tricornutum can be a new Aβ fluorescent imaging reagent in AD diagnosis.