Previous studies on crustacean diversity in Panguil Bay, a rich fishing ground in Mindanao (Jimenez et al., 2009), only focused on adult individuals. Larval and juvenile stages, which are also frequently encountered in the area, have been largely overlooked in biodiversity estimates or are often not included in species descriptions because these stages are difficult to identify accurately. Aside from the limited identification keys available for these life stages, other constraints include shared meristics, overlapping morphological characters, and high phenotypic plasticity (Raupach and Radulovici, 2015), making identification more challenging. Accurate species identification is a critical component in many research topics, including biodiversity studies and conservation planning and thus, a faster and more reliable method is needed to supplement and confirm traditional morphology-based identification. In recent years, the use of DNA barcodes (mitochondrial DNA cytochrome oxidase I or mtDNA COI) was proven to be successful at identifying different metazoans, including crustaceans (Hebert et al., 2003). In this study, we aim to identify larval and juvenile stages of crustaceans (particularly shrimps and crabs) in Panguil Bay using the mtDNA COI marker. The results of this study could be used as a reference for the management of these resources in the future.