Live cell imaging by fluorescence microscopy is a useful tool for elucidating the localization and function of proteins and organelles in single cells. Especially, time-lapse analysis observing the same field sequentially can be used to observe cells of many organisms and analyze the dynamics of intracellular molecules. By single-cell analysis, it is possible to elucidate the characteristics and fluctuations of individual cells, which cannot be elucidated from the data obtained by averaging the characteristics of an ensemble of cells. The primitive red alga Cyanidioschyzon merolae has a very simple structure and is considered a useful model organism for studying the mechanism of organelle division, since the division is performed synchronously with the cell cycle. However, C. merolae does not have a rigid cell wall, and environmental changes such as low temperature or high pH cause morphological change and disruption easily. Therefore, morphological studies of C. merolae typically use fixed cells. In this study, we constructed a long-term time-lapse observation system to analyze the dynamics of proteins in living C. merolae cells. From the results, we elucidate the cell division process of single living cells, including the function of intracellular components.