Elucidating the intricate interplay between microorganisms and crops, mainly maize (Zea mays), holds promise for devising agronomic interventions to augment yield, inducing defense mechanisms against pests and pathogens, and alleviating abiotic stresses. In pursuit of comprehending the composition of the maize root microbiomes across different genotypes, we conducted a thorough characterization of the root and rhizosphere microbiome of three indigenous Ecuadorian Andean maize cultivars, UCE-Amarillo, INIAP-122, and UCE-Pepa grown in a native soil, employing high-throughput DNA sequencing targeting the 16S rRNA gene. Root tissues and rhizosphere were collected from 18 plants from each cultivar, plus 18 bulk soil samples. Alpha diversity metrics, such as the Chao and Shannon indices, were employed to assess microbial richness and evenness, revealing a notably lower diversity within the root microbiome than the rhizosphere and bulk soil compartments. Furthermore, discernible plant genotype-driven microbiome assembly patterns were observed across all compartments. Taxonomic profiling unveiled a conspicuous absence of Actinobacteria and an elevated abundance of Proteobacteria within the root microbiome. Moreover, 34 amplicon sequence variants (ASVs) were present in all the root and rhizosphere samples (100% occupancy) from the three cultivars, making these the core microbiome of the indigenous Ecuadorian Andean maize. The highly consistent root and rhizosphere colonization across cultivars make these 34 ASVs great candidates as bioinoculants for maize in the Andean region of Ecuador. Target isolation and functional characterization of these microbes are necessary for future applications to enhance their resistance to biotic and abiotic stresses.