Atopic dermatitis (AD) is a chronically relapsing pruritic inflammatory skin disease. To find new anti-inflammatory products for skin inflammatory disease such as AD and contact dermatitis, we produced the effective microorganism fermentation substance (EM-S) by fermentation of medicinal plants with effective microorganisms including photosynthetic bacteria, lactic acid bacteria and yeast, screened the effects of EM-S on NC/Nga model mice. Murine AD-like skin lesions were made by painting Dermatophagoides farinae (Df) extract. Topically applied EM-S significantly reduced clinical severity score, ear thickness and histological grade in AD-like NC/Nga mouse model by Df antigen sensitization. In addition, the serum IgE and Th2 chemokine levels (TARC/CCL17, MDC/CCL22 and CTACK/CCL27) were significantly reduced by EM-S. Futhermore, skin tissue expressions of Th2 chemokines were significantly reduced by EM-S. These results demonstrate that topical application of EM-S may be improve the AD-like skin lesion by suppressing IgE and Th2 chemokines.