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Abstract Wireworms are recognized as economically important oligophagous pests of Phyllostachys bamboo shoot, which have caused a huge economic loss in South China. Studies of bamboo shoot wireworm control and management were seriously hampered by the lack of reliable identification of larvae. DNA barcoding has been proved to be an important and useful tool in species identification of morphologically cryptic insects. Accurate knowledge of damage-causing species and the phylogenic structure of elaterids will provide insight into their sustainable and effective management. Here, we use interspecific variation in COI and EF1-a as a robust method of identification and consider the intra- and interspecific genetic variation of bamboo wireworms. This approach has revealed that three Melanotus larvae occurred in Phyllostachys forest. The dominance of one species in different sampling location suggests there maybe underlying difference in habit and host plant preference. These data provide a starting point for determining the distribution of wireworm species feeding on bamboo shoots in South China. The inclusions would further aid identification of wireworm species and relationships between certain wireworm species with specific environments. Graphical abstract Unlabelled Image Highlights • Both mitochondrial and nuclear markers help in wireworm identification. • Three species of bamboo shoot wireworms were identified in South China. • Melanotus cribric ollis (Faldermann) proved to be dominant in bamboo forests. • Significant genetic differentiation was found in each bamboo shoot wireworm species. [ABSTRACT FROM AUTHOR]