Alnus acuminata ssp arguta (Schlect.) FURLOW (Betulaceae) is a monoecious, nitrogen fixing pioneer tree species, that occurs throughout Latin America, from central Mexico to northern Panama. 17 natural populations (54 trees/population on average) were sampled from Costa Rica and Panama. Genetic variation was assessed at putative gene loci coding for 10 isoenzyme systems. Only 4 gene loci were polymorphic. Average polymorphism (16 %), number of alleles per polymorphic locus (2.0), allelic diversity (1.29) and average heterozygosity (4 % for all loci, and 22 % for polymorphic loci) were very low in comparison to other Alnus species and other tropical trees species. Cluster analysis revealed a pattern of genetic variation associated with geography for most populations. Genetic differentiation among populations, even within the same geographical region, was larger than reported previously for other Alnus species. Repeated bottlenecks due to its early successional behavior and its association to natural catastrophies, interspaced by periods of population expansion, are the main pattern shaping the population dynamics of this species. Low gene flow, due to partial geographical isolation among and within regions, may contribute to the relative large population differentiation (11% overall gene differentiation among populations was detected, with over 5 % due to among populations within same geographical region and over 5.5 % among regions). Idh-A showed the largest genetic differentiation among populations and regions (15 %). The last glacial and interglacial events possibly played an important role for the re-establishment of migration and gene flow among the disjuncted regions of Alnus occurrence throughout Latin America.