The scope of this study was to enumerate and identify microorganisms present in crude oil polluted soil before and after remediation with Eudrilus eugeniae using conventional method for enumeration and molecular tools (ITS 1 and ITS 4 primers) for identification. A crude oil polluted soil from Khana Local Government of Rivers State Nigeria and also soil from botanical garden of the University of Lagos were used. These soil samples were measured in four different concentrations (25%, 50%, 75% and 100%). Each of these concentrations was experimental setup of addition of substrate alone, E. eugeniae and substrate and E. eugeniae alone. These setups were made in triplicate amounting to a total of thirty six experimental setups. Enumeration of microbial load was done before and after addition of each of the content of the experimental setups using conventional method and then identification of microbes was done using molecular tools. The result shows total heterotrophic fungi was 2.9 x 10 4 cfu/m/g, while the total heterotrophic bacteria was 4.4 x 10 5 cfu/m/g before remediation. After remediation, total heterotrophic fungi was 1.6 x 10 5 cfu/m/g while total heterotrophic bacteria was 5.0 x 10 4 cfu/m/g. This shows that microorganisms were present in the soil before and after remediation. The increase in number of microbes suggests a favorable condition for continuity of microbial life. Fungi such as Trichoderma asperellum, Aspergillus flavus, Penicillum chrysogenum and another strain of Aspergillus flavus were identified. The bacteria sequencing failed suspected to be due to primers used or error with sequencing plates. In conclusion, the results of this study confirmed the presence of microorganisms in crude oil polluted soils. The enumeration and identification of the bacteria and fungi in this experiment will help to enhance in situ clean-up of crude oil polluted soil.