At present time, chemical fertilizers are more in practice for crop production, which failed to upkeep soil and environment quality and affected the sustainability of the agricultural production system. Conversely, biofertilizers are ecosystem friendly, one of the best modern tools for agriculture, and are used to improve soil fertility and quality. Biofertilizers have now emerged as a highly potent alternative to inorganic fertilizers and offer an ecologically sound and economically attractive route for augmenting nutrient supply and increasing crop production. These include live cells of diverse genera of microorganisms and have the potential to fix atmospheric nitrogen and solubilize and mobilize plant nutrients from insoluble form through microbiological process. It has also the potential to diminish the gap between nutrient supply through fertilizers and nutrient removal by crops. Hence, biofertilizers can be a feasible option to the farmers to increase crop productivity and should find greater acceptance from the extension workers and commercial biofertilizer manufacturers. Applications and Constraints of Plant Beneficial Microorganisms in Agriculture DOI: http://dx.doi.org/10.5772/intechopen.89190 atmospheric nitrogen, which is transformed into organic nitrogenous compound. The nitrogen-fixing bacteria work under two conditions, symbiotically (Rhizobium, Frankia) and as free-living bacteria (nonsymbiotic) such as Azotobacter and Azospirillum. The N 2 -fixing bacteria associated with nonlegumes include species of Achromobacter, The most exploited symbiotic N 2 -fixing bacteria are those belonging to the family Rhizobiaceae. Rhizobium inoculants are of greatest importance because of their ability to fix atmospheric N 2 in association with certain legumes [11]. It is estimated that N 2 fixation by Rhizobium in root nodules of legumes is of the order of 14 million tons on a global scale and is almost 15% of the industrial N fixation. Yield of many legumes can be increased substantially by the use of appropriate Rhizobium cultures. For successful nodulation each legume requires a specific species of Rhizobium to form effective nodules. Many legumes may be modulated by diverse strains of rhizobia, but growth is enhanced only when nodules are produced by effective strains of rhizobia [12]. Rhizobium can be used for legumes crop and trees (e.g., lucerne) and is a crop-specific inoculant, for example, Rhizobium trifolii for berseem, Rhizobium meliloti for lucerne, Rhizobium phaseoli for green gram and black gram, Rhizobium japonicum for soya bean, Rhizobium leguminosarum for pea and lentil, Rhizobium lupini for chickpea, and Rhizobium spp. for cowpea. Rhizobium is however limited by cross-inoculation group, and only certain legumes are benefited by this symbiosis.Similar to the Rhizobium, other filamentous bacteria of genus Frankia belonging to the family Frankiaceae are found in the root nodules of nonlegumes such as trees and shrubs. These bacteria live in symbiosis with actinorhizal plants. These actinorhiza...