Zhu1S is an elite indica thermo-sensitive genic male-sterile breeding stock widely used in hybrid rice production in Southern China. To improve the key agronomic traits of this elite cultivar, somatic mutagenesis method was used to screen for semi-dwarf mutations. The phenotypic and preliminary molecular characterization of two somatic mutants, named SV1S and SV14S, was reported. Compared with the parent Zhu1S, these mutations have reduced plant statures, shortened and thickened the lower internodes significantly but the upper internodes slightly. Furthermore, we have found an approximate 200 bp deletion in the GA20ox-2 gene encoding the key GA metabolic enzyme and little transcription of this gene in both semi-dwarf mutant lines. These results have indicated that SV1S and SV14S mutants are more likely impaired in gibberellin metabolism derived from the same mutation, which is partially responsible for their semi-dwarf phenotype. However, both mutants have similar height at the seedling stage and slightly reduce the GA sensitivity of amylase activity in aleurone cells, which is different from the previously reported sd-1 mutants. Therefore, it is assumed that there is a second-site mutation in the SV mutants. Our results have further demonstrated the usefulness of somatic mutagenesis in the rice breeding program.