Bacteria and fungi are good indicators for soil health as well as soilless growing media (SGM) health. However, there is very limited information about the fungal and bacterial communities for SGM. In the present study, coir substrate and peat-based substrate were used as typical SGM under drip irrigation and tidal irrigation to understand the situation of fungal and bacterial communities by high-throughput sequencing technology. In this study, both environmental factors and microbial communities were significantly affected by SGM type and irrigation pattern, in which SGM type played a major role and irrigation pattern played a minor role. The bacterial phyla Actinobacteriota and Proteobacteria and the fungal phyla Ascomycota were more closely related to environmental factors including EC, pH, NO₃⁻, NH₄⁺ and ω as well as urease and phosphatase. The bacterial and fungal communities in the two SGM had some similarities with those in soil. In addition, the functions of the soil, including key soil organisms, carbon mineralization, wood decomposition, nitrification, denitrification, carbon fixation, nitrogen fixation and methanotrophy, could be basically performed by the two SGM. In general, the SGM should possess common soil capabilities according to bacterial and fungal analyses, but there are numerous fungi of unknown function that need be addressed in the future. Meanwhile, these results improve our understanding of the correlation between the environmental factors and the microbiome, and provide basic guidance for management and research on SGM in the future.