A variety of simple culture-based tests which are proposed to recover a wide range of microorganisms from water are collectively known as heterotrophic plate count (HPC) and used as an indirect indicator to give information about water quality.  The aim of this study was to assess the heterotrophic plate count (HPC) culture-based dependent and 16S rRNA independent techniques of identifying bacteria. The HPC was conducted by incubating a filtered sample of water on R2A agar plates and enumerating the number of resultant bacterial colonies that grow on each plate. The molecular analysis was performed by extracting the deoxyribonucleic acid (DNA) from bacterial isolate and polymerase chain reaction (PCR) was done to obtain the amplicons (PCR products). Purified PCR products were sequenced by ABI V3.1 Big dye kit and the analysis of sequence was conducted by the basic local alignment search tool (BLAST) to identify their closest relatives. A total number of 17 isolates of Pseudomonas, Bacillus and Proteus were phenotypically identified, while the nucleotide sequence revealed the presence of 59 diverse strains with distribution (percentage) of Pseudomonas (25) 42.2 %, Bacillus 17 (28.8 %) and Proteus (17) 28.8 %. The investigated isolates when compared from gene data-base recorded genetic relatedness with similarity index of 61 to 100 %. The 16S rRNA gene sequences from DNA extractions showed microbial consortia in drinking water to comprise of a broad array of bacterial diversity, including those of critical concern to human health such as Pseudomonas and Bacillus. Finally, there was no significant correlation between the HPC test and 16S rRNA sequence analysis.