The peroxidase and esterase isozymes of the germplasm resources of Houttuynia in Sichuan were analyzed. The results showed that it existed plentiful isozymes variations among the germplasm resources of Houttuynia in Sichuan. The cultivated populations had the same isozymes band types as the wild ones. There were 6 different types of peroxidase isozymes bands and 10 different esterase isozymes band totally. Each peroxidase band type was composed of 4 to 6 bands, and esterase isozymes had 5 to 8 bands. There was no significant difference between Houttuynia cordata and Houttuynia emeiensis populations in their isozymes bands types. The results also showed that the number of peroxidase isozymes bands in northern areas was somewhat higher than that in southern areas. However, esterase isozymes band types had no geographic differences.