A precise and comprehensive assessment of species diversity is fundamental and crucial across many biological studies. However, delimiting species through a morphological approach remains challenging, especially when samples are incomplete or degraded in the repository museum or when morphological variation is high because of phenotypic plasticity, which has been commonly observed among marine gastropods. Inventory studies on marine gastropods in Malaysia showed a record of 384 species, a surprisingly far smaller number compared to other regions within the same high biodiversity region. The molecular approach, through high-throughput sequencing, is increasingly used to obtain taxonomic information on targeted organisms. Unfortunately, genome skimming approaches for marine gastropods from Malaysia were scarce, and the emerging environmental DNA (eDNA) approach as a future biodiversity monitoring tool also remained unexplored. In this study, the shelled gastropods collected from the selected intertidal coastal area of Peninsular Malaysia were identified morphologically and then sequenced through high-throughput sequencing using group-specific primers (16S and CO1). Sample vouchers were kept at the South China Sea Natural History Museum, Universiti Malaysia Terengganu. This study flags an important effort in constructing a DNA barcode library for this taxon within this geographical region. Subsequently, the phylogenetic tree of the marine gastropod species in Malaysia was constructed to understand their evolutionary relationship. The research is important for biodiversity monitoring in Malaysia, specifically on marine gastropods, and could potentially be applied to other taxa. This study will contribute to the National Policy on Biological Diversity 2016 to 2025 using a cost-effective tool for maintaining the sustainable use of natural resources.