Studying the process of population restoration is helpful for managing and preserving endangered species. A population of Oryza rufipogon (wild rice), an endangered species, was reintroduced in 1993 into Huli Marsh. We conducted a detailed survey over a 5-year period (1997–2001) to evaluate the present status of the population and to further our understanding of its habitat requirements and the population model. The population was surveyed using 2 × 2–m quadrats in mid-September of each year. In total, 2,683 quadrats were surveyed covering the whole O. rufipogon reserve during each survey. The population's spatial distribution was mapped, and the maps were used to examine the relationship between patch replacement and water depth. The individual number of O. rufipogon increased steadily from 1993 to 2001. The patch number, patch area, mean patch size, and largest patch size increased over this time period, and Korcak patchiness exponents decreased. On average, 83% of the patches persisted from one year to the next. There was a significant positive correlation between the initial patch size and the size the following year. The probability of patch disappearance decreased as patch size increased. Fifty-eight percent of the patches were located at water depths between 20 and 30 cm. Water depth had no significant effect on the patch transition from O. rufipogon to other species. The loss and gain of O. rufipogon patches were statistically correlated with the patch areas in different water depths. Our results show that the population of O. rufipogon can successfully be reintroduced to the original habitat after appropriate environmental conditions have been restored. We recommend the following transplantation practices: transplant many smaller patches rather than a few larger patches, use transplant patch sizes of at least 20 m2, and transplant into sites vegetated with species with different regeneration niches from the transplanted species.