The exposure of crops to a variety of fungal and bacterial diseases leads to their huge losses both in quantity and quality. Different strategies are being adopted to control of these diseases among which the use of chemical pesticides is a common one. But the health risk due to chemical exposure is being associated with this common method. The application of biological control antagonists (BCAs) can provide a positive plus promising alternative to chemicals. Many mycelial fungi and bacteria have proved to be good antagonists against several plant pathogens, but less literature is available, in contrast, for the use of yeasts as biological antagonists. This study was an effort to evaluate the biocontrol efficiency of indigenous endophytic yeasts associated with healthy plants against different root rot pathogens. Hundred yeast strains were isolated from different vegetative parts of healthy plants belonging to seven genera. Out of hundred yeasts tested, sixty-nine isolates showed inhibitory effect during in vitro assay against Fusarium solani, F. oxysporum, and Macrophomina phaseolina, to varying degrees. Maximum inhibitory effect against root rotting fungi was observed by yeast strains KUAY-17, KUAY-34, KUAY-62. Out of hundred yeast isolates, sixty-nine isolates repressed the mycelial growth of the three tested fungi viz., Fusarium solani, F. oxysporum and Macrophomina phaseolina. No yeast was effective against Rhizoctonia solani during in vitro testing. KUAY-34, 62 and 66 caused maximum inhibition of F. solani while F. oxysporum was greatly suppressed by KUAY-9, 25, 34, 38 and 62. Mycelial growth of M. phaseolina was restricted greatly by KUAY-5, 9, 34 38 and 62. Eleven yeast isolates showed 100% nematicidal activity against second stage juveniles of root knot nematodes after 48 hours, while other strains killed the juveniles to varying degrees. Out of 15 isolates tested for Indole Acetic Acid production, 2 yeast isolates produced maximum concentration of IAA in vitro, whereas, all the tested yeast isolates exhibited the phosphate solubilization property. The effective yeast strains were subjected to testing for their biocontrol activity in screen house experiments using Sunflower (Helianthus annuus L.), Mungbean (Vigna radiata (L.) Wilczek) and Tomato (Lycopersicon esculentum Mill.) as test crops. The yeasts were able to inhabit the roots of test crops when applied externally to plants in sterilized soil. They significantly enhanced the growth of tested plants. In soil, having naturally infestation of root rotting fungi, the application of endophytic yeasts not only reduced the incidence of pathogens but also promoted the plant growth. Out of 17 tested yeast isolates, 4 isolates, viz., KUAY-5, KUAY-17, KUAY-34 and KUAY-62 exhibited great potential of reducing fungal pathogens along with the promotion of plant growth both in screen house experiments as well as under field conditions. The combined treatment of yeasts and neem cake had positive impact on plants growth and on the suppression of fungal pathogens. The application of yeast isolate KUAY-62 also increased the nodulation in the roots of mungbean plants. A notable increase was observed in the phosphorus uptake and antioxidant activity in the plants treated with endophytic yeasts. Induction of Systemic Acquired Resistance (SAR) in the plants have an imperative role in fighting with pathogens. In the current study, the application of endophytic yeasts improved the status of phenolic compounds and salicylic acid in the test crops which contributed towards the obliteration of pathogens and promotion of plant growth under field conditions.