Abstract: This study explored the relationships between genetic and morphological characteristics of Ophiopogon japonicus using 25 samples collected from different areas of the Sichuan Basin. Peroxidase isozyme (POD) was studied using vertical slab polyacrylamide gel electrophoresis (PAGE) and the zymograms were analyzed using SPSS software version 13.0. There were 10 different POD band types and each band type was composed of 6 to 11 bands. There was no significant difference in POD band type between erective and creepy morphotypes. The band type was different between materials collected in the same area but with different morphological characteristics. There were plentiful POD variations among the germplasm resources of O. japonicus in the Sichuan Basin. The genetic relationship was not associated with geographical distributions, but was obviously related to the morphological characteristics. POD characteristics could be considered as a significant reference base in the classification of the germplasm materials of O. japonicus, and could be used to determine the genetic difference and relationships of the germplasm materials.