The population genetics and phylogeography of Trema dielsiana in Taiwan were inferred from genetic diversity at the nonsymbiotic hemoglobin gene and the trnL-trnF intergenic spacer of cpDNA. Reduced genetic variation was detected in these two unlinked genes. The gene genealogy of the hemoglobin locus recovered two lineages corresponding to the western and eastern regions of Taiwan. This pattern is compatible with a past fragmentation event revealed by phylogeographical analyses. To distinguish between selective departures from neutrality (i.e., heterogeneous processes) and demographic (homogeneous) processes, Hahn et al.'s heterogeneity test was conducted on the hemoglobin gene. Lack of significant differences in Tajima's D statistics between synonymous and nonsynonymous mutations indicates that homogeneous processes may have played a key role in governing the evolution of the functional locus. Significantly negative Tajima's D estimates for both overall exons and introns of the hemoglobin gene as well as for the cpDNA intergenic spacer support a phylogeographical hypothesis of range expansion after genetic bottlenecks. High level of genetic variation and a negative Tajima's D statistic suggests a possible northern refugium that may have harbored populations during the glacial maximum.