The study of the origin of underwater artefacts is a crucial and relevant topic to be highlighted, especially in the Southeast Asia Region, due to the active trading route during the Age of Sail. In the present study, we aim to discover the ship type and sailing route of the Bidong shipwreck using both relative and absolute analysis. The team analysed the wood samples collected at the Bidong shipwreck site during the second excavation phase. The analysis of wood anatomy and Deoxyribonucleic Acid (DNA) was performed on five wood fragments at the Forest Research Institute Malaysia (FRIM). Based on the conducted analyses, two types of trees were identified in the construction of Bidong shipwrecks, namely Giam (Hopea spp.) and Meranti Temak Nipis (Shorea roxburghii). Both types of trees are commonly discovered in tropical climate regimes and the area of the Malay Archipelago. In addition, the team also compared the selected artefacts from the first phase of excavation with some published references of Southeast Asian Ceramic and live records from National Maritime Museums, Chanthaburi, and Southeast Asian Ceramic Museum, Bangkok University, Thailand. Significantly, the comparison analysis suggests that the artefacts rescued from the Bidong shipwreck were Thai ceramics of the Maenam Noi (Singburi) and Si Satchanalai (Sawankhalok) types. The result from these studies suggests that the Bidong shipwreck stopped loading Siamese ceramics or even repairing in Southeast Asia and sailing along the east coast of Peninsular Malaysia for some destination in the sixteenth century during the Age of Monsoonal Civilisation.