Determination of the minimum population size is an important component for the ex situ conservation of an endangered species. Here, we present the identification of collection strategies that most efficiently captured the genetic diversity of Brasenia schreberi J.F. Gmelin (water-shield) in natural populations from the mainland (MGC) and Jeju Island (JNS) of South Korea, using amplified fragment length polymorphism (AFLP) markers. A total of 313 and 383 polymorphic bands were detected in the MGC and JNS populations, respectively. All of the 140 sampled ramets were distinguishable by the presence of distinct AFLP phenotypes. According to the simulation of the individual sampling by maximization sampling, 25 and 28 individuals captured all of the genetic diversity in the MGC population (mainland of South Korea) and the JNS population (Jeju Island), respectively. The level of genetic diversity of the core collections was similar to the entire collection, indicating that the core collections very well represent the diversity of the entire collection. We therefore suggest a management unit of B. schreberi based on the genetic information for assessing the minimum population size for its ex situ conservation.