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Genetically modified crops are already successfully grown worldwide in more than 18 countries on more than 67 million hectares which increases annually by more than 10%. Nigeria, in October 2018 joined the many other countries by approving Bacillus thuringiensis (Bt) cotton and maize, therefore, there was the need to carryout environmental risk assessment studies. A total of fifteen (15) four litter (4L) octagonal ceramic pots were filled with four kilograms (4Kg) of soil and placed on bench in two rows of ten pots each and a third row of five pots. First row pots were used to plant GM cotton seeds, while the second row pots were used for non GM cotton seeds and a third row of five pots served as control, all in the screen house. The GM cotton seeds were collected from National Biosafety Management Agency, Abuja while the non GM cotton seeds were collected from seed bank of Tissue Culture Unit of NABDA. Soil samples for metagenomic DNA extraction were collected at random and at monthly interval after planting at a distance of 2mm to 5mm from plant’s root and at a depth of 5cm to 10cm using sterile spatula. The DNA was extracted using Zymobiomic soil DNA extraction kit, nano drop technique and gel electrophoresis were used to confirm the DNA before sequencing. Sample 1A (DNA from GM cotton Soil at first interval) gave the lowest sequence read with 0.853M while sample 2B (DNA from GM cotton Soil at second interval) gave the highest with 5.785M, others gave between 1.8M and 4.7M. The samples treatment were grouped into four, Group 1 (GM cotton soil from 1 to 3 intervals), Group 2 (non GM cotton soil from 1 to 3 intervals), Group 3 (control soil) and Group 4 (initial soil). The microbes observed were predominantly bacteria (including archaea), fungi, dark matter alongside protists and phages with focus on the phages community. The predominant phages were, Acinetobacter virus, Bacillus virus SPbeta, Hpunavirus_u_s, Staphylococcus phage, Paenibacillus phage, Enterobacteria phage and Stenotrophomonas phage. The comparative analysis between groups was done using JACCARD PERMANOVA beta diversity analysis at P – value not more than 0.68 and there was no significant pair found. The results suggest that, the GM crops have no significant effect on phage ecology of the soil and in turn no direct or indirect effects on human health.