Cyanobacteria are the simplest organisms to exhibit circadian rhythms, which have been exclusively studied in the unicellular strain, Synechococcus. Since Anabaena is one of the simplest multicellular organisms harboring both regular pattern formation with cell differentiation and presumably circadian rhythms, it provides an excellent model to address following questions: 1) difference in the kaiABC functions and output pathways between Synechococcus and Anabaena; 2) clock systems in vegetative cells and heterocysts; 3) synchronization of neighboring clock cells; and 4) circadian modulation of heterocyst differentiation/patterning. Surprisingly, in contrast to the highest amplitude cycle of Synechococcus kaiBC mRNA, none of Anabaena kai genes showed significant expression rhythms, while we found ~200 clock-controlled genes. It suggests striking differences in clock and clock-controlled gene expression mechanism between the two species. Nevertheless, by using bioluminescence reporters to monitor rhythmic gene expression, we confirmed that both strains have similar circadian properties in terms of temperature compensation of the period and phase-response curves against dark-pulses.