Cell wall invertase (CWIN) are known to play important roles in seed development. However, most reports to date have focused on a single gene family member, and have mainly investigated CWIN functions during the filling stage of seed development. In this study, we found significant lower levels of CWIN protein and activity associated with seed abortion in the Litchi chinensiscultivar “Nuomici.” We identified five litchi CWINgenes and observed that the expression of LcCWIN5was limited to the flower tissues and decreased sharply with fruit development. Silencing of LcCWIN5expression before 28 DAA (cell division stage) resulted in perturbed liquid endosperm development, smaller seeds, and higher seed abortion rate, while silencing after 28 DAA (filling stage) had no effect on seed development. In contrast, LcCWIN2was mostly expressed in the funicle and seed coat, and increased with fruit development. Decreased LcCWIN2expression and CWIN activity during early seed filling coincided with smaller seeds in the cultivar “Feizixiao.” Silencing of LcCWIN2caused a reduction in the seed size without inducing seed abortion. We propose that CWIN activity in seed maternal tissues during cell division stage is likely due to LcCWIN5expression, which regulates early seed development. On the other hand, CWIN activity during the filling stage is due to the expression of LcCWIN2, which may promote carbon import by creating a sucrose gradient. Comparable LcCWIN5expression, but much lower CWIN activity, detected in the funicle of “Nuomici” is consistent with post-translational regulation. A family of genes, known as cell wall invertases (CWINs), control different stages of seed development in litchi, and could be used to breed more desirable fruits. Seed set and seed size are important characteristics of horticultural plants, with the seeds of some crops being significant food sources, while seedlessness or small seededness is sought after in many fruit crops. A team led by Jietang Zhao and Huicong Wang, of South China Agricultural University, studied the genes controlling seed set and size in small-seeded, large-seeded and seed-abortive cultivars of litchi (Litchi chinensis). They identified five members of the CWINfamily, of which one, LcCWIN5, was shown to regulate early seed development, while another, LcCWIN2, was active during the later “seed-filling” stage. These results could aid the development of more attractive, small-seeded or seedless varieties of litchi.