Using the qPCR, we studied the effects of intercropping of watermelon (Citrullus lanatus (Thunb.) Matsum & Nakai) with wheat (Triticum aestivum L. Poaceae family) on the abundances of total bacteria, beneficial microbes (Pseudomonas, Bacillus, Streptomyces, Actinomycetes and Trichoderma spp.) communities, total fungi, pathogenic microbes [(Fusarium oxysporum, Fusarium oxysporum f.sp. niveum (FON)] and allelochemicals 2,4-diacetylphloroglucinol (DAPG), phenazine-1-carboxylic acid (PCA) and pyrrolnitrin (PRN) producers in watermelon rhizosphere. The intercropping decreased the abundances of Pseudomonas and Actinomycetes spp., DAPG, PCA and PRN producers at 20 d, and later increased the PCA and PRN producers at 30 d and 40 d. The intercropping with wheat increased the abundances of total bacteria, Pseudomonas spp., Streptomyces, Actinomycetes and Trichoderma spp., and reduced those of total fungi, Bacillus spp., Fusarium oxysporum and FON at 40 d. These results indicated that intercropping of wheat + watermelon affected the microbial communities and increased the abundances of allelochemicals producing genes in watermelon rhizosphere.