Abstract <p>In bacteria and some eukaryotes, an important tool to respond to both external and internal signals is a two-component system, which is typically composed of a transmembrane receptor histidine kinase (RHK) and its cognate response regulator. While architecture and distribution of RHKs in prokaryotes are well-documented, their roles in eukaryotes, particularly in the green algae, remain less understood. Here, we analyzed the sequences and domain architectures of RHKs within the green algae clade <i>Chlorophyta</i>, in the class <i>Chloropicophycea</i>e, better characterized compared to other classes. Our study aims to deepen understanding and infer the biological roles of these proteins. Based on InterProScan results, we showed that rhodopsin-histidine kinases play a global role in the biology of the microalgae: they dominate among all RHKs, representing 57% of them. The length variation of RHKs does not have a discrete structure. Furthermore, we identified the most frequent domains and domain architectures in the proteins, with a notable discovery of a significant number of hybrid histidine kinases, where the sensory domain is a microbial rhodopsin protein. We demonstrate also that one-half of the identified rhodopsin-histidine kinases possess a catalytic domain of either adenylyl or guanylyl cyclase, making them potentially useful as optogenetic tools. In addition, it is shown that a significant part of RHKs in green algae contain not one but two REC-domains. These findings, along with previous reports, suggest that multiple REC-domains may support complex regulatory functions, possibly allowing condition-dependent responses. Our work may also help to understand better RHKs potential in optogenetics.</p>