Studies of genetic variation can elucidate the structure of present and past populations as well as the genetic basis of the phenotypic variability of species. Taxodium distichum is a coniferous tree dominant in lowland river flood plains and swamps of the southeastern USA which exhibits morphological variability and adaption to stressful habitats. This study provides a survey of the Mississippi River Alluvial Valley (MAV) and Florida to elucidate their population structure and the extent of genetic differentiation between the two regions and sympatric varieties, including bald cypress (var. distichum) and pond cypress (var. imbricatum). We determined the genotypes of 12 simple sequence repeat loci totaling 444 adult individuals from 18 natural populations. Bayesian clustering analysis revealed high levels of differentiation between the MAV and the Florida regions. Within the MAV region, there was a significant correlation between genetic and geographical distances. In addition, we found that there was almost no genetic differentiation between the varieties. Most genetic variation was found within individuals (76.73 %), 1.67 % among individuals within population, 15.36 % among populations within the regions, and 9.23 % between regions within the variety. Our results suggest that (1) the populations of the MAV and the Florida regions are divided into two major genetic groups, which might originate from different glacial refugia, and (2) the patterns of genetic differentiation and phenotypic differentiation were not parallel in this species.