Abstract To understand the seed softness character in pomegranate (Punica granatum L.) fruit, we have studied gene expression associated to cell wall formation in the seed of soft- and hard-seeded pomegranate genotypes at five different stages from fruit set to ripening. For this purpose, some cell wall formation related genes were isolated and identified from pomegranate and their expression patterns were compared in two soft- and hard-seeded genotypes. The results showed that for some of the cell wall biosynthesis genes the expression levels increased at stages where the seed cover was becoming hard, then decreasing gradually during fruit ripening. CCR and CAD, two specific monolignol biosynthesis genes, showed higher expression in the hard-seeded genotype during the critical stages of seed hardening, but COMT, a specific S-unit monolignol, showed a completely different pattern with higher expression in the soft-seeded genotype. Cellulose synthesis -related genes (CelSy and SuSy) showed higher expression in the soft-seeded genotype at critical stages of seed development. However, EGase had higher expression at early stages and rapidly decreased to the undetectable level during fruit development, and CHS, another phenylpropanoid gene, showed no significant variation over time. The differences between seed hardness was detectable at 60 DAF in the soft- and hard-seeded genotypes. The lignin and cellulose content increased in the seeds of both genotypes during fruit development. The soft-seeded pomegranate had lower lignin content, while had relatively higher amount of cellulose compared to the hard-seeded one. These results suggest that lignin and cellulose have complementary roles in the cell wall structure of pomegranate seed. Taken together, our data suggest that the difference between the ratio of S to G monolignols could be the main cause of the seed softness in pomegranate.