A geographical traceability system for Merbau (Intsia palembanica Miq.), an important timber species from peninsular Malaysia

•A geographical traceability system for Merbau (Intsia palembanica Miq.), an important timber species from peninsular Malaysia.•Genetic databases were developed for the important tropical timber species Merbau, Intsia palembanica.•The comprehensive databases included 39 natural populations of Merbau from throughout peninsular Malaysia.•The analysis of a combination of 4 cpDNA and 14 STR markers classified the populations into northern and southern regions of peninsular Malaysia.•Our databases contribute to the verification of geographical origin and to combating illegal logging associated with the species. To inform product users about the origin of timber, the implementation of a traceability system is necessary for the forestry industry. In this study, we developed a comprehensive genetic database for the important tropical timber species Merbau, Intsia palembanica, to trace its geographic origin within peninsular Malaysia. A total of 1373 individual trees representing 39 geographically distinct populations of I. palembanica were sampled throughout peninsular Malaysia. We analyzed the samples using a combination of four chloroplast DNA (cpDNA) markers and 14 short tandem repeat (STR) markers to establish both cpDNA haplotype and STR allele frequency databases. A haplotype map was generated through cpDNA sequencing for population identification, resulting in six unique haplotypes based on 10 informative intraspecifically variable sites. Subsequently, an STR allele frequency database was developed from 14 STRs allowing individual identification. Bayesian cluster analysis divided the individuals into two genetic clusters corresponding to the northern and southern regions of peninsular Malaysia. Tests of conservativeness showed that the databases were conservative after the adjustment of the θ values to 0.2000 and 0.2900 for the northern (f = 0.0163) and southern (f = 0.0285) regions, respectively. Using self-assignment tests, we observed that individuals were correctly assigned to populations at rates of 40.54−94.12% and to the identified regions at rates of 79.80−80.62%. Both the cpDNA and STR markers appear to be useful for tracking Merbau timber originating from peninsular Malaysia. The use of these forensic tools in addition to the existing paper-based timber tracking system will help to verify the legality of the origin of I. palembanica and to combat illegal logging issues associated with the species.