As the demand for oil and its byproducts rises across the world, the supply of traditional crude oil is steadily dwindling. In order to keep up with energy demands, oil corporations are pumping out crude oil from older fields, where traditional primary and secondary recovery has left more than 60% of reserves untapped (Zhang et al. Crit Rev Biotechnol 40:459–474, 2020; Shibulal et al. Sci World J 2014:1–12, 2014). To raise the total productivity of oil from matured oil reservoirs, it is necessary to create an inexpensive and effective enhanced oil recovery (EOR) technique, such as chemical, thermal, microbiological, or miscible EOR, to generate this residual oil. One of the techniques used in the tertiary recovery stage is called Microbial Enhanced Oil Recovery (MEOR). Heavy oil is notoriously difficult to remove from oil reservoirs due to its high viscosity and limited flow characteristics. Microbial EOR is the new emerging area in the field of EOR as it combines green chemistry with lower carbon footprint. The nonpathogenic fungi like mycorrhiza, Trichoderma sp., Penicillium sp., Fusarium sp., Phoma sp. etc. have been identified as an source of rhamnolipids, Sophorolipids that produces the various natural surfactants commonly called “Biosurfactants”. By decreasing the interfacial tension between the oil and water, a biosurfactant solution can free the oil that has been trapped by capillary forces interface and hence found application in enhanced oil recovery. In this chapter we have focused on the application of various non pathogenic fungi in enhanced oil recovery.