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In this study, different maize fields cultivated under different management systems were sampled to test corn leaf aphid, <i>Rhopalosiphum maidis</i>, populations in terms of total and endosymbiotic bacterial diversity. Corn leaf aphid natural populations were collected from traditionally managed maize fields grown under high agricultural and natural landscape diversity as well as conventionally treated high-input agricultural fields grown in monoculture and with fertilizers use, hence with low natural landscape diversity. Total bacterial community assessment by DNA sequencing was performed using the Illumina MiSeq platform. In total, 365 bacterial genera were identified and 6 endosymbiont taxa. A high abundance of the primary endosymbiont <i>Buchnera</i> and secondary symbionts <i>Serratia</i> and <i>Wolbachia</i> were detected in all maize crops. Their frequency was found to be correlated with the maize management system used, probably with fertilizer input. Three other facultative endosymbionts (“<i>Candidatus Hamiltonella</i>”, an uncultured <i>Rickettsiales</i> genus, and <i>Spiroplasma</i>) were also recorded at different frequencies under the two management regimes. Principal components analyses revealed that the relative contribution of the obligate and dominant symbiont <i>Buchnera</i> to the aphid endosymbiotic bacterial community was 72%, whereas for the managed system this was only 16.3%. When facultative symbionts alone were considered, the effect of management system revealed a DNA diversity of 23.3%.