Freshwater species are the most threatened group to be assessed to date by the IUCN. Freshwater fish has enormous importance as animal protein supplies for human, and it is estimated that 6% of the world annual animal protein supplies come from freshwater fishes. Barcoding projects have been initiated all over the world and the field is constantly growing. In Malaysia however, the field has not been deeply investigated and not many barcoding projects have been undertaken especially for freshwater fishes. The aim of our study is to support the progress of DNA barcode project, especially for inland reservoirs like Tasik Raban, Perak. A Standard methodology using Cytochrome c oxidase subunit 1 (COI) marker was developed to ensure native fishes are barcoded taxonomically and molecularly and ready to be accessed through online databases. Such public references can help increase awareness on local fish diversity management. Information on taxonomy and molecular characterization can be used to plan further conservation programmed especially for depleted, unrecognized, and cryptic native species.