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The damaging competition between crops and parasitic weeds has a negative impact on agricultural productivity; however, the impact of disturbance on the soil’s microbial community has received less attention. Hence, this study investigates the microbial composition and diversity of the maize rhizosphere infected with Striga hermonthica using a shotgun sequencing approach from two maize-growing fields (Eruwa, Nigeria and Mbuzini, South Africa). The rhizosphere soil DNA was extracted from infested soil using a Nucleospin soil genomic DNA extraction kit and sequenced on an Illumina platform. The dominant phyla were Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Acidobacteria, Chloroflexi, Cyanobacteria, Planctomycetes, Verrucomicrobia, Chlorobi, Proteobacteria, Firmicutes, Nitrospirae, Thermotogae, Synergistetes, Ascomycota, Euryarchaeota, and Crenarchaeota. Bacteria phyla were observed to be of higher proportion in the rhizosphere soil samples obtained from Striga-infested maize field in Eruwa (Es) than those recovered from Mbuzini (Ms). The alpha diversity of microbial communities indicated insignificance differences (p > 0.05) between the five taxonomical groups (phylum, class, order, family, and genus), while the beta diversity produced a significant (p = 0.01, R = 0.52) difference in the microbial diversity of the infested soil. In summary, the study sheds light on the diversity and composition of the microbiome of Striga hermonthica-infested soil, which influences the microbial functions in the management and sustenance of plant health against parasitic weeds.