Agricultural sustainability is one of the core agendas, and on this, a massive amount of research has been conducted worldwide. Microbes have been considered as one of the key components of this agenda, as they can substitute the agrochemicals that have been used in agricultural farms for last many decades. Various microbes have been isolated from different niches that have been found beneficial. Rhizosphere, mycorrhizosphere, and hyphosphere are distinct niches of microbes. These niches harbor diversity of microbial species belonging to bacteria and fungi, which helps in promoting the plant growth and development. Microbes harboring these specific niches promote the growth of plants through plant growth-promoting (PGP) mechanisms, i.e., direct and indirect, which help in providing the required nutrients, phytohormones, and protection. Mechanisms including solubilization (phosphorus, zinc, potassium), fixation (nitrogen), chelation of iron through siderophores production, antibiotic production, secretion of hydrogen cyanide, and hydrolytic enzymes are the various PGP mechanisms. These microbes that exhibit PGP activities can be used as biopesticides and biofertilizers for agricultural sustainability. This chapter complies the diversity inhabiting the rhizosphere, mycorrhizosphere, and hyphosphere niches and their molecular mechanisms for plant growth.