We assessed genetic diversity and structure in the outcrossing orchid Goodyera rosulacea, endemic to limestone regions in Korea. Using allozymes as genetic markers, standard genetic diversity measures within and among populations as well as genetic structure were estimated. In addition, a regression analysis between pairwise genetic and geographical distances and correlation analyses between population sizes and estimates of genetic variation within populations were conducted to gain insights into the past evolutionary processes. Moderate levels of genetic variation were found in the species (%P_s = 31.6%, A_s = 1.37, H_es = 0.126); at the population level, slightly lower levels were estimated (%P_p = 27.8%, A_p = 1.31, H_ep = 0.100). Overall fixation index was not significantly different from zero (F_IS = 0.160). As compared with that in most terrestrial orchids, the measure of genetic differentiation among populations was also moderate (F_ST = 0.150). At the regional scale, a weak linear regression between pairwise genetic and geographical distances was found, suggesting that populations are not at equilibrium between gene flow and genetic drift (i.e., little evidence of isolation-by-distance effect). A significant correlation between population size and mean number of alleles per locus was detected (p = 0.006). These results suggest that genetic drift, coupled with limited seed dispersal, has played an increasing role in the genetic dynamics of small populations, though outcrossing breeding system might have in part counterbalanced against these negative effects. Threats to the species are considered to be anthropogenic. In situ and ex situ conservation strategies are suggested to preserve the genetic variation in the rare G. rosulacea.