Centromere dynamics are largely unknown in lower plants (algae). We have recently identified the centromere-specific histone H3 variant (CENH3) and clarified the dynamic centromere rearrangement at mitosis in the primitive red alga Cyanidioschyzon merolae. We also showed that the CENH3-containing nucleosomes constituted the kinetochore closely interacting with the nuclear envelope. CENH3 visualization during the whole cell cycle suggests that C. merolae centromeres are monocentric and confined to specific loci. We completed 100% no-gap telomereto-telomere sequencing of the C. merolae genome. Interestingly, a single A+T-rich region has been identified on each fully sequenced chromosome. No centromere-like A+T-rich repetitive sequence have been found within these regions, implying that the C. merolae centromeres may be ‘point’ centromeres, or be comprised of nonrepetitive heterogeneous DNA sequences.