Background and aims <p>The rhizosphere microbial community plays a fundamental role in plant health, which is related to its production capacity when it comes to agricultural plants. In this work, wheat (<i>Triticum aestivum</i>) genotypes from a reference mapping population were selected to analyze how plant genotype and developmental stage can modulate the assembly and composition of the plant-rhizobiome. Likewise, the relevance of rhizosphere microbial communities in the nitrogen pathway was analyzed.</p> Methods <p>Fourteen selected wheat genotypes in three stages of development were used for this experiment. Total DNA from the rhizosphere was extracted and sequenced for the 16S and 18S rRNA. Likewise, the abundance of genes involved in key steps of the nitrogen cycle was estimated.</p> Results <p>The bacterial communities associated with the fourteen selected wheat genotypes rhizosphere were dominated by phyla Pseudomonadota, Actinomycetota, Bacillota, Bacteroidota, and Acidobacteriota. In the case of fungi communities, the main phyla were Ascomycota, Basidiomycota, and Mucoromycota. Finally, the N₂ fixation (<i>nifH</i>) and denitrification (<i>nirS</i>, and <i>nosZ</i>) genes increased in the last stage of development analyzed.</p> Conclusion <p>The data suggest that the microbial community is modulated by genotype and evolves similarly in related genotypes during the different stages of development.</p>