The genetics of small population size is of considerable interest to conservation biologists and land managers concerned with maintaining genetic diversity in populations of rare plants. In this paper, I present evidence obtained through starch gel electrophoresis of allozymes that an isolated population of Cleistes bifaria (Fern.) Gregg and Catling is multiclonal with levels of genetic diversity comparable to other taxa in the Orchidaceae. A total of 24 unique multilocus genotypes were resolved by eight alleles expressed by three polymorphic loci in a census of 64 aboveground stems. Levels of clonal diversity and evenness in the distribution of genotypes indicate that the population rapidly responds to favorable habitat conditions maintaining allozyme diversity despite repeated population contractions to few reproductive individuals. Sixty stems (35 flowering) had appeared in a newly created field after only five years with allozyme and clonal diversity mirroring that found in a long-existing habitat. The population genetic data obtained from allozymes plus population monitoring and knowledge of site history suggest that intrapopulation genetic variation is maintained within persistent individual clones that apparently survive underground during periods of adverse environmental conditions.