Levels of allozyme variation, population genetic structure, and fine-scale genetic structure (FSGS) of the rare, endangered terrestrial orchid Pogonia minor were examined for three small and isolated populations (n = 185) in South Korea using 20 putative allozyme loci resolved from 14 enzyme systems. Of the three populations, only one was polymorphic at four loci. Thus, extremely low levels of allozyme variation within populations were found: mean percentage of polymorphic loci was 6.7%, mean number of alleles per locus was 1.07, and mean expected heterozygosity was 0.015. Polymorphic population exhibited a significant deficit of heterozygotes relative to Hardy-Weinberg expectations (F_IS = 0.257), suggesting selfing (rate, s = 0.349) through autogamy and biparental inbreeding. Analysis of O-ring function revealed significant aggregation of individuals suggests restricted seed dispersal and patchy distribution of microhabitats within populations. Spatial autocorrelation analyses revealed a significant fine-scale genetic structure (up to ≤ 2 m) within a polymorphic population, and a significantly high degree of population differentiation was found among populations (F_ST = 0.196). These results suggest that genetic drift, coupled with inbreeding, limited gene dispersal and founder effects would be the main explanatory factors for the extremely low levels of genetic diversity and for shaping the population genetic structure of P. minor in South Korea. Considering the current genetic structure of P. minor, in situ and ex situ conservation of the known populations of the species is suggested.