Formosan alder (Alnus formosana (Burk.) Makino), a deciduous native tree in Taiwan, has dominant colonizing ability in open areas from lowland up to 2,500 m. The genetic structure of twenty-two populations of this species was studied by allozyme electrophoresis analysis. In the fifteen enzymes surveyed, 59.1 % of the loci was found polymorphic and the mean effective number of alleles per locus 1.21. The proportion of genetic diversity among the populations studied was 0.02 and the genetic distance among populations ranged between 0.000 to 0.019 with a mean of 0.004. Low genetic differentiation in Alnus formosana may be attributed to high degree of gene flow. However, the significant correlations between allelic frequencies in four loci and the altitude gradient revealed partial genetic variation that correlated with temperature differences.