In plants, neither the contribution of the plasmotype in controlling circadian clock plasticity and overall plant robustness, nor what may be the fitness consequences of clock plasticity on genetic make-up has been fully elucidated. Here, we investigated the cytonuclear genetics underlying thermal plasticity of clock rhythmicity and fitness traits in reciprocal doubled haploid population and a diversity panel of wild barley ( Hordeum vulgare ssp. spontaneum). We identified a positive correlation between the thermal plasticity of clock and vegetative growth with the robustness of reproductive output. Moreover, we identified significant linkage disequilibrium and epistatic interactions between previously identified drivers of clock (DOC) loci and the chloroplastic RpoC1 genes, indicating adaptive value for specific cytonuclear gene combinations. Finally, heterologous over-expression of two barley RpoC1 alleles in Arabidopsis showed significantly differential plasticity under elevated temperatures. Our results unravel previously unknown cytonuclear interactions as well as specific alleles within the chloroplastic genome that control clock thermal plasticity while also having pleiotropic effects on plant fitness in the field. The evolutionary and functional relationship between nuclear and chloroplastic DOCs suggest that adaptation to warming environments involve cytonuclear changes to confer local adaptation.