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Chlamydomonas reinhardtii (C. reinhardtii) is one of the most important microalgae model organisms and has been widely studied towards the understanding of chloroplast functions and various cellular processes.Further exploitation of C. reinhardtii as a model system to elucidate various molecular mechanisms and pathways requires systematic study of gene regulation. However, there is a general lack of genome-scale gene regulation study such as global cis-regulatory element (CRE) identification in C. reinhardtii. Recently, large-scale genomic data in microalgal species have become available, which enable the development of efficient computational methods to systematically identify CREs and characterize their roles in microalgae gene regulation. Here we performed in-silico CRE identification at the whole genome level in C. reinhardtii using a comparative-genomics-based method. We identified a large number of CREs in C. reinhardtii that are consistent with experimentally verified CREs. We also discovered that a large percentage of these CREs form combinations and have the potential to work together for coordinated gene regulation in C. reinhardtii. Multiple evidences from literature, gene transcriptional profiles and gene annotation resources support our discovery. The discovered CREs will serve as the first large-scale collection of CREs in C. reinhardtii to facilitate further experimental study of microalgae gene regulation.