The Ikogosi Warm Spring is a unique ecological niche in Western Nigeria with an average temperature and pH of 38˚C and 5.8 respectively. It mixes with an adjacent cold spring (28˚C & pH 7.6), about 100 meters from source, yielding a confluence body of water of 32˚C and pH 7.7. To explore the bacterial community structure of this uncommon environment and to scan for potentially useful bacteria, metagenomes extracted directly from five samples (source and mid-point of warm spring; source and midpoint of cold spring, and the confluence) were analyzed. Using the MiSeq Illumina next generation sequencing protocols, the V3-V4 region of the 16S rRNA gene pool was sequenced and analyzed by QIIME (Quantitative Insights into Microbial Ecology) and R software. At least 11% (47,446) of all the sequences were unknown to any of the databases employed. Bacterial diversity and abundance at the source of both springs were extremely low, accounting for less than 0.07% of the total sequence reads at the confluence, 100 m downstream. In contrast to the highly diversified mesophilic confluence community where 21 different phyla were identified, only 4 and 5 phyla were recovered from the source-point of the warm spring and cold spring respectively. The most prevalent phyla in all samples were members of the versatile Proteobacteria (35%-50% relative abundance), and the hardy Firmicutes (33%-40%). Operational taxonomic units (OTUs) obtained from all the samples averaged at 1414. Temperature and pH were equally significant predictors of genomic diversity and richness, with the warm and cold spring sources having less than 5 bacteria phyla. Exiguobacterium sp. (a potential plastic degrader) and other deep rooted bacteria were found in the warm spring while the cold spring outflow contained among others such asRubrobacter sp. and Chloroflexi sp. (which is close to the phylogenetic root of the domain Bacteria