Plants effectively defend themselves against biotic and abiotic stresses by synthesizing diverse secondary metabolites, including health-protective flavonoids. These display incredible chemical diversity and ubiquitous occurrence and confer impeccable biological and agricultural applications. Chalcone synthase (CHS), a type III plant polyketide synthase, is critical for flavonoid biosynthesis. It catalyzes acyl-coenzyme A thioesters to synthesize naringenin chalcone through a polyketidic intermediate. The functional divergence among the evolutionarily generated members of a gene family is pivotal in driving the chemical diversity. Against this backdrop, this study was aimed to functionally characterize members of the CHS gene family from Rheum emodi, an endangered and endemic high-altitude medicinal herb of northwestern Himalayas. Two full-length cDNAs (1,179 bp each), ReCHS1 and ReCHS2, encoding unique paralogs were isolated and characterized. Heterologous expression and purification in Escherichia coli, bottom-up proteomic characterization, high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry analysis, and enzyme kinetic studies using five different substrates confirmed their catalytic potential. Phylogenetic analysis revealed the existence of higher synonymous mutations in the intronless divergents of ReCHS. ReCHS2 displayed significant enzymatic efficiency (V max /K m ) with different substrates. There were significant spatial and altitudinal variations in messenger RNA transcript levels of ReCHSs correlating positively with metabolite accumulation. Furthermore, the elicitations in the form of methyl jasmonate, salicylic acid, ultraviolet B light, and wounding, chosen on the basis of identified cis-regulatory promoter elements, presented considerable differences in the transcript profiles of ReCHSs. Taken together, our results demonstrate differential propensities of CHS paralogs in terms of the accumulation of flavonoids and their relative substrate selectivities.Plants, as ground-anchored sessile creatures, invest significant amounts of energy in the production of secondary metabolites to combat environmental pressures. These metabolites often are produced through complex and highly regulated biosynthetic pathways under the influence of different enzymatic machineries. One of the important classes of secondary metabolites is phenylpropanoids. These represent a significant proportion of secondary metabolites, encompassing nearly 20% of total carbon in the terrestrial biosphere. Flavonoids exhibit remarkable chemical diversity and ubiquitous occurrence and play an important role in many aspects of plant development, like flower coloration, photoprotection, pollen development, cell wall growth, and response to stress conditions like UV light protection, herbivory, wounding, interaction with soil microbes, and defense against pathogens (Yu and Jez, 2008;Pandey et al., 2015). Apart from performing numerous imperative roles in plants, flavonoids also have been reported as poten...