In this study we report the kinetics of photoacclimation of the unicellular alga Nannochloropsis sp. grown under high light (HL), and subsequently transferred to low light (LL). We examined the changes in ultrastructural features, pigmentation, and photosynthetic parameters over short intervals until the LL steady state was reached. The ultrastructural changes were followed by quantitative morphometric measurements of transmission electron micrographs. We found that the increase in the relative volume of the chloroplast during acclimation to LL (twofold) was accompanied by an increase in number of stacks (twofold) and in the surface area of thylakoids per cell (2.5‐fold). The increase in photosynthetic unit (PSU) density was about 2.15‐fold. Maximal density was about 84 PSU·μm−2 in LL cells, and minimal density was 39 PSU·μm−2 in HL cells. The HL/LL ratio of the in vivo optical absorption cross‐section of PSU (σPSU) was 2.8, whereas in the in vivo optical absorption cross‐section of the cell (σcell), the trend of change was in the opposite direction: 1.7‐fold higher in LL‐acclimated cells than in HL‐acclimated cells. We propose a partial sequence of the photoacclimation processes based on our data and the derived rate constants.