Regarding the rising rate of esophageal cancer in some parts of Asia, including northern and northeastern regions of Iran, the identification of new anti-cancer compounds is essential to combat the disease. The relation between some plants metabolites and these endophytic microorganisms are well characterized. In the current study, the potentials of Ephedra endophyte bacteria for the inhibition of esophageal cancer cell line (KYSE-30) proliferation were investigated. A total of 54 endophyte bacteria (out of 70) were obtained from the sterilized surfaces of two medicinal plants, i.e., Ephedra intermedia and Ephedra foliata. Bacterial strains were then cultured in Tryptic soy broth (TSB) medium and, after 72 h incubation, the produced secondary metabolites were extracted by chloroform. Anticancer effects of secondary metabolites from theses bacteria on esophageal cancer cell line KYSE-30 were evaluated after 24, 48 and 72 h by MTT method. MTT assay results showed that only strain A1 had a cytotoxic effect on KYSE-30 cells. The IC₅₀ amounts of this strain against KYSE-30 cell lines were equaled (µg/ml) to 346.4, 192.8 and 121.3 after 24, 48, and 72 hours, respectively. The molecular identification of strain A1 revealed that Microbacterium maritypicum (99.8% similarity) was the closest identified taxon to the strain studied. According to the promising ability of strain A1 to inhibit the growth of KYSE-30 cell line, the use of natural compounds produced by this bacterium to treat esophageal cancer was found to be applicable. However, more experiments are needed to confirm these results after purifying the ingredients, as well as conducting studies in animal cancer models.