Plant growth tests were performed with radish (Raphanus sativa var. radicula Pers.) in culture solutions containing low molecular weight compounds in the presence of aluminum to determine the types of functional groups in kraft lignin (KL) modified with ozone and alkali that contributed to reducing aluminum toxicity. The low molecular weight compounds used in this study contained carboxyl, formyl, methoxyl, alcohol hydroxyl, and phenolic hydroxyl groups. The compounds that had adjacent two carboxyl groups (oxalic acid), carboxyl/alcohol hydroxyl groups (glycolic acid), or carboxyl/formyl groups (glyoxylic acid) were effective in reducing aluminum toxicity. Malonic acid, having two carboxyl groups, also reduced aluminum toxicity. The ability of ozone-treated KLs to reduce aluminum toxicity was considered to be partly due to these chemical structures. Protocatechuic acid, having two adjacent phenolic hydroxyl groups, was also effective in reducing aluminum toxicity. This indicated that the effectiveness of the alkaline-treated KL was partly due to its catechol structure.