Circadian rhythms play a key role in transcriptome regulation in photosynthetic eukaryotes. Circadian gene expression patterns can anticipate daily changes in light and orchestrate the appropiate metabolic and developmental responses. CircadiaNET consists of three different gene co-expression networks that integrate RNA-seq and microarray data generated over 24 h periods in neutral day conditions (12 h light / 12 h dark) from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri. Evolution and conservation of different circadian gene expression patterns is analyzed in CircadiaNet combining a new tool for potential orthologues identification, Multiple Bidirectional Best Hit (MBBH) and gene expression data. Using this approach CircadiaNet can assist researchers to define specific gene clusters or modules regulated by the circadian clock that are involved in particular biological processes assesing their conservation/evolution over the green lineage. This could allow researchers to make predictions on gene function and dissect the mechanisms that conform present day plants physiology.