Since regulatory roles of calcium (Ca) and melatonin (MT) in physiological responses of plants to salinity stress are lacking, various Dracocephalum kotschyi genotypes (Bojnord, Urmia, Fereydunshahr, and Semirom) were pretreated with exogenous Ca (5 mM), MT (100 μM), and Ca + MT in the presence of salt (75 mM NaCl). In addition measuring the concentration of phenolic compounds by high-performance liquid chromatography (HPLC), histochemical evaluations of essential oils and phenolic compounds in glandular trichomes of leaf samples was performed by light microscope. Salt stress reduced shoot fresh (SFW) and dry weight (SDW), leaf area (LA), relative water content (RWC), and maximum efficiency of photosystem II (F v /F m ), but enhanced total phenolic content (TPC) and total flavonoids content (TFC), phenolic compounds concentrations, 2,2-diphenylpicrylhydrazyl (DPPH) radical scavenging capacity, electrolyte leakage (EL), proline, and hydrogen peroxide (H 2 O 2 ) concentrations, and Na + /K + and essential oils and TPC of the glandular trichomes of leaves in all D. kotschyi genotypes. Foliar spraying of Ca, MT, and particularly Ca + MT on D. kotschyi seedlings improved SFW, SDW, RWC, TPC, TFC, proline, and phenolic compounds concentrations, F v /F m , and DPPH radical scavenging capacity, but reduced H 2 O 2 , EL, and Na + /K + in the leaves and essential oils and TPC in the glandular trichomes of all genotypes under both nonstress and salt stress conditions. These findings indicate that the crosstalk between MT and Ca synergistically improves salt tolerance, TPC and TFC, phenolic compounds concentration, and essential oils accumulation in glandular trichomes of different D. kotschyi genotypes.