Identification of microorganisms, including bacteria, are widely used especially in environmental studies, biotechnology, clinical microbiology, microbial forensics, and in research study. The conventional method of bacteria identification is based on phenotypic observation techniques by profiling an organism’s metabolic attributes or some aspect of its chemical composition. Then, interpretation of test results involves substantial subjective judgement. Currently, general 16S rRNA sequencing and specific PCR play an important role in the accurate and faster identification of bacteria. The aim of this study is to compare the identification of the genus or species of bacteria from agricultural waste using conventional microbiology biochemical test and molecular techniques PCR 16S rRNA universal amplified ribosomal region (UARR) sequencing. A total of 72 agricultural waste samples and 2 ATCC culture as positive control were tested. Out of two ATCC bacteria and fifteen bacteria isolates identified by the biochemical test, twelve species (71%) of bacteria gave exactly the same bacteria genus as the 16S rRNA sequencing results. Aeromonas hydrophilia, Alcaligenes faecalis and Acinetobacter calcoaceticus was revealed as Pseudomonas sp. from the sequencing results. As for Alcaligenes sp., the results from the sequencing is Stenotrophomonas maltophilia. Previous reports also showed different results of the same isolate which were from similar classification, and closely related to each other. The limited number of biochemical tests available in a laboratory will contribute to misidentification of a proposed specie.