Melatonin (N-acetly-5-methoxytryptamine) is a secondary metabolite produced by plants, animals and microorganisms. Plants produce melatonin to ameliorate the negative impacts of exposure to various abiotic and biotic stressors. To date, a very limited number of studies focusing upon the roles of melatonin in microbes have been conducted, the findings of which indicate that melatonin may have a similar ameliorative effect upon stress exposure in microbes as observed in plants. The aim of this study is to examine the effects of melatonin on soil microbial community structures and to identify microbes whose development is modified. Melatonin and indole-3-Acetic acid (IAA), a structurally similar indoleamine, was applied to a sandy loam (sodosol) soil at the concentrations of 1, 100 and 750 µM, and incubated at room temperature for up to two weeks. The microbial community fingerprint of the bacterial and fungal communities present in the soil in response to the treatments were assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA). Melatonin and IAA treatments resulted in similar and significant shifts in both fungal and bacterial soil community structures after one week, with species richness and evenness negatively impacted. PCR amplification and sequencing using universal fungal and bacterial primers resulted in the preliminary identification of several microbes that were enriched after melatonin and auxin application. The implications for the modification of soil community structures by melatonin and the identification of the microbes involved will be highlighted.