An allozyme analysis was conducted to determine the population genetic structure of baldcypress (Taxodium distichum [L.] Rich. var. distichum) and pondcypress (Taxodium distichum var. imbricarium [Nuttall] Croom) and the level of genetic differentiation between these two taxa. Approximately 400 individuals of both varieties and apparent morphological intermediates were sampled from 21 locations across the geographic range of Taxodium distichum and 11 enzyme loci assayed by starch gel electrophoresis. Although baldcypress populations contain higher levels of genetic variation among sub-populations, populations of both varieties have approximately the same levels of heterozygosity. Populations of baldcypress and pondcypress were found to differ on the basis of varying allele frequencies of one locus, PGI-2, which appears to be semi-diagnostic as a varietal indicator. A correlation was observed between the allele frequencies of this locus and a ratio of bark thickness to diameter (BT/D). Baldcypress exhibits higher frequencies of PGI-2 allele “1” and lower BT/D ratios, whereas pondcypress has higher frequencies of PGI-2 allele “3” and higher BT/D ratios. An apparent clinal gradient was observed in the spatial distribution of both BT/D ratios and PGI-2 phenotypes within a few populations. The apparent existence of gene flow (whether it is presently occurring or has occurred in the recent past) and the possibility of clinal variation within populations suggest that these two taxa are best regarded as varieties of the same species.