The epigenetic control of gene expression by histone methylation influences plant growth and development. OsiEZ1, encoding a putative histone methyltransferase for trimethylation of histone H3 lysine 27 (H3K27me3), was recently shown to be involved in the photoperiodic control of rice flowering. However, to date, the role of OsiEZ1 in organ development has not been characterized in detail. Here, we show that the loss of OsiEZ1 results in abnormal ligule and seed development. Morphological analysis showed that the ligules in flag leaves of the T-DNA insertion mutant osiez1 were shorter than those of the wild-type, whereas plant height and flowering time in the mutant were similar to those of the wild-type. In addition, the seed size and weight of the osiez1 mutant were reduced compared with those of the wild-type. Expression analysis showed that the transcript levels of the GRAIN WIDTH 2 (GW2) gene and chaperone protein gene PROTEIN DISULFIDE ISOMERASE-LIKE 1-1 (PDIL1-1) were reduced in the osiez1 mutant compared with the wild-type during seed development, while the expression levels of seed storage protein genes Glb and Gt were unchanged in the osiez1 mutant. These results suggest that OsiEZ1 may play important roles in ligule and seed development.