Abstract The present research aimed to investigate Loka Pere banana (Musa sp.), an endemic species with distinct characteristics, but currently underrepresented in scientific literature. Our primary goal was to isolate the Internal Transcribed Spacer (ITS2) region from the leaf and corm samples of this unique banana variant. As a methodological approach, we utilized a modified CTAB protocol to extract DNA and amplified the ITS2 region via polymerase chain reaction (PCR) using ITS-S2F and ITS-S3R primers, achieving an amplicon size approximately 500 bp long. The results showed successful isolation of the ITS2 sequences from both leaf and corm samples of Loka Pere Banana. This finding signifies the potential of the ITS2 region of the Loka Pere banana as a novel and reliable DNA barcode marker. Future research can leverage this data for more accurate molecular identification and phylogenetic analyses, enhancing our understanding of the genetic diversity among the Musa genus.