We investigated the root microbiomes of rice sampled from six major rice-producing regions in Ghana using Illumina MiSeq high-throughput amplicon sequencing analysis. The result showed that both bacterial and fungal community compositions were significantly varied across the regions. Bacterial communities were shaped predominantly by biotic factors, including root fungal diversity and abundance. In contrast, fungal communities were influenced by abiotic factors such as soil nitrate, total carbon and soil pH. A negative correlation between the diversity and abundance of root fungi with soil nitrate (NO₃^-) level was observed. It suggested that there were direct and indirect effects of NO₃^- on the root-associated bacterial and fungal community composition. The gradient of soil nitrate from North to South parts of Ghana may influence the composition of rice root microbiome. Bacterial community composition was shaped by fungal diversity and abundance; whereas fungal community composition was shaped by bacterial abundance. It suggested the mutualistic interaction of bacteria and fungi at the community level in the rice root microbiome. Specific bacterial and fungal taxa were detected abundantly in the ‘Northern’ regions of Ghana, which were very low or absent from the samples of other regions. The analysis of indicator species suggested that an ‘ecological specialization’ may have occurred which enabled specific microbial taxa to adapt to the local environment, such as the low-nitrate condition in the Northern regions.