Gobiocypris rarus, an endemic cyprinid fish with high fecundity, lives mainly in small water systems easily influenced by changes in natural surroundings. This study used 11 polymorphic microsatellite primers to identify the temporal variation of its topotype population. Moderate genetic diversity, inbreeding phenomena, and limited temporal variation between 1997 and 2006 were revealed in the topotype population. The main temporal fluctuations involved only the change of allelic frequencies over two loci and allelic richness. The effective population size was estimated to be 645. The authors argue that inbreeding did not induce dramatic depression effects on the topotype population, and the forces to maintain genetic diversity were mainly from environmental fluctuations and life history traits. Considering that the topotype population is facing increased habitat loss, destruction, and disturbance due to human activities, the authors suggest that a habitat and species management area be established in the type locality.