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Insects are under constant selective pressure, which has resulted in adaptations to novel niches such as crops. This is the case of the pest <i>Melanaphis sacchari</i>, the sugarcane aphid, native to Africa and currently spreading worldwide. The aphid undergoes successful parthenogenesis, causing important damage to a variety of crops and leading to important economic losses for farmers. A natural <i>M. sacchari</i> population grown in sorghum was studied to identify its microbiome through the sequencing of its 16S rDNA metagenome. A high proportion of Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria, was observed. We also detected <i>Wolbachia</i>, which correlates with the asexual reproduction of its host. <i>M. sacchari</i> was challenged in a bioassay with the antibiotics oxytetracycline and streptomycin, resulting in a dose-dependent decay of its survival rate. The possibility of controlling this pest by altering its microbiota is proposed.