Agar and gellan gum have been considered to have different effects on polyploidy-dependent growth in plants. We aim to demonstrate that agar and gellan gum differently affect the change in root elongation in Arabidopsis thaliana by polyploidization and examined the physico-chemical parameters in each gelling agent to elucidate key factors that caused the differences. Each polyploid strain was cultured vertically on agar and gellan gum solidified medium under fixed conditions. Root elongation rate was measured during 4-10 days after sowing. As a result, agar promoted root elongation of polyploids more than the gellan gum. Then water potential, gel hardness, and trace elements of each medium were quantified in each medium. Water potential and gel hardness of agar medium were significantly higher than those of gellan gum medium. The decrease in water potential and gel hardness in agar medium, however, did not affect the change in polyploidy-dependent growth. Elemental analysis showed that gellan gum contained more aluminum than agar. Subsequently, the polyploids were grown on agar media with additional aluminum, on which the root elongation in tetraploids and octoploids was significantly suppressed. These results revealed that agar and gellan gum affect the change in growth of root elongation in A. thaliana by polyploidization in different ways and the different effects on change in polyploidy-dependent growth is partially caused by aluminum in the gellan gum, which may be due to cell wall composition of polyploids.