Food allergy (FA) and atopic dermatitis (AD) are representative allergic diseases that begin early in life and result in considerable socioeconomic burden. While the pathophysiology and the optimal treatment modalities of these diseases are largely unknown, the role of microbes in health and disease are being highlighted. Recent advances in analyzing microbiome have enabled us to expand our research on impacts of the microbiome on the onset and course of FA and AD. Risk factors that are presumed to affect intestinal microbiome also modulate the onset of allergic diseases, which is more evident in AD than in FA. Considering animal studies, intestinal microbiota interacts with FA and the influence is bi-directional. The activation of regulatory T cell and the innate immune system is supposed to mediate the interaction. Regarding human studies, there exists the difference in the composition of microbiome between subjects with FA or AD and matched normal controls, which can further play as a predictive marker for later development of FA or AD. Probiotics are now investigated as a primary therapeutic agent or as an adjuvant tool for conventional therapies in preventing or modulating FA or AD. Currently, several reports on favorable outcomes become available, which should be replicated and backed up by large-scale studies with more detailed protocols.