There are studies on the assessment of non-edible transgenic plants on soil microbial communities. In this research we evaluated the effect of virus-resistant trigonal cactus on soil microbial communities of the rhizosphere. Soil samples are collected and compared in genetically modified (GM) and non-GM trigonal cactus cultivation fields during vegetative growth period and post-harvest period. Biolog EcoplateTM was used to evaluate the functional diversity of soil microbial communities. There were no significant differences between the GM and non-GM soil samples collected during the vegetative growth period. However, we observed temporary difference in carbon substrate utilization. Principal component analysis showed that soil microbiota was influenced not by presence of GM or non-GM trigonal cacti, but rather by the cultivation period. Denaturing gradient gel electrophoresis fingerprinting revealed that virus-resistant trigonal cactus cultivation had insignificant effect on soil microbial communities including dominant rhizosphere bacteria, actinomycetes, and fungi. We found no clear evidence of GM trigonal cactus cultivation affecting the functional diversity of soil microbial communities.