The traditional rice-fish farming system is selected as a "globally important agricultural heritage system" (GIAHS) by the Food and Agriculture Organization (FAO), United Nations Development Programme (UNDP), and Global Environment Facility (GEF), etc. In Zhejiang Province of China, where the pilot site for this GIAHS farming system is located, we compared the use of traditional rice varieties in rice-fish co-culture and rice monoculture. Further, we determined how traditional rice varieties were performed in this rice-fish system. Only 19% of the farmers who practiced rice monoculture planted traditional varieties while 52% of farmers who practiced rice-fish co-culture planted traditional varieties. Traditional varieties represented 13% of the total land cultivated under rice in the rice-fish system but only 2% in the rice monoculture system. In the rice-fish system, yield was lower for traditional rice varieties than hybrid varieties but application of fertilizers and pesticides was also lower. In a field experiment in the rice-fish system without pesticides, rice planthopper numbers and sheath blight incidence were lower from three traditional varieties than one hybrid variety; yields were 8 to 32% lower from the traditional varieties than the hybrid. Our results showed that traditional rice varieties can be preserved through conserving GIAHS rice-fish co-culture. Our study also indicated that traditional rice varieties can survive in the rice-fish system because these varieties are helpful to the whole system and beneficial to the farmers.