Fungal abundance and diversity in soils of three communities flow stations (ID, IR and OB) owned by an unnamed oil exploration firm operating in the Niger Delta area for about five decades were determined using nucleic acid analytical methods. Top soil (0-15 cm) samples were collected from mini pits using sterile bottles at 50, 100 and 150 meters from the flare barrier of each community flow station and soil samples from the control was taken at 2.5 kilometers during the dry and wet seasons. The fungal properties were determined first using the cultural method of serial dilution method which revealed the presence of the following fungi; Aspergillus sp, and penicillium chrysogenum at 50 m away from flare in all the three flow stations during the dry seasons and in the wet season Aspergillus sp, penicillium chrysogenum, Mucor sp., yeast cells, A. niger, and Rhizopus sp. At 100 m away from flare, Mucor sp, A. niger and rhizopus were isolated in all three-flow station in the dry season and in the wet season, Yeast cells, A. niger, Aspegillus sp. and Rhizopus were isolated. P. chrysogenum, Aspergillus sp. and yeast cells were isolated at 150 m away from flare in the dry season and in the same distance, yeast cells, A. niger aggregate, A. niger and P. chrysogenum were isolated. At the control site, during the dry season, A. niger, P. chrysogenum, Aspergillus sp., Rhizopus sp. and Botryodiplodia threobome were isolated in the dry and A. niger, P. chrysogenum and yeast in the wet season. Fungal DNA was extracted using Norgen fungal genomic DNA extraction kits for the molecular analysis to establish the true characteristics and species identity of the isolates earlier identified with cultural methods. This revealed the presence of the following fungi upon sequence blast on NCBI database; Aspergillus fumigatus (Aspergillus fumigatus brown 2 (abr2) gene, complete cds strain), Aspergillus fumigatus (Aspergillus fumigates strain IHM 15988 pigment biosynthesis protein), Fusarium phyllophilum , Fusarium graminearum, Aspergillus oryzae (a strain of Aspergillus niger) Aspergillus oryzae (niger). Findings from this work have shown that molecular technique gave the exact identity of fungal species isolated from study area. All six (6) molecularly identified fungi were isolated from the three-study flow station and in both seasons. The Aspergillus group was dominant as a result of their ability to adapt to the flare environment and all isolated fungi are good crude oil degraders.