The enzyme p-hydroxyphenylpyruvate dioxygenase (HPPD) is very important in prenylquinone biosynthesis in all photosynthetic organisms. In this study, we present the functional characterization and expression analysis of HPPD from the unicellular green alga Chlamydomonas reinhardtii P. A. Dang. Recombinant HPPD1 enzyme was purified and characterized. Kinetic analysis revealed a Km of 49 μM for p-hydroxyphenylpyruvate, similar to other HPPDs. The size of HPPD subunit was estimated as 47 kDa by SDS-PAGE, in accordance with the predicted molecular size after HPPD1 cDNA sequence. However, native HPPD1 enzyme showed an apparent molecular mass of 188 kDa and a homotetrameric structure, which suggests a reconsideration of the idea that all eukaryotic HPPDs have a homodimeric structure while all prokaryotic HPPDs are homotetramers. Expression analysis by Northern blot revealed that hppd1 expression is strongly up-regulated by low temperature and poorly regulated by high temperature, darkness, or moderate light changes, suggesting that Chlamydomonas HPPD may play an important role in the synthesis of tocopherols and/or plastoquinones under stress conditions in the physiological context of the adaptation to growth at low temperatures.