Early embryo development from the zygote is an essential stage in the formation of the seed, while seedling development is the beginning of the formation of an individual plant. AtNSE1 and AtNSE3 are subunits of the structural maintenance of chromosomes (SMC) 5/6 complex and have been identified as non-SMC elements, but their functions in Arabidopsis growth and development remain as yet unknown. In this study, we found that loss of function ofAtNSE1andAtNSE3led to severe defects in early embryo development. Partially complemented mutants showed that the development of mutant seedlings was inhibited, that chromosome fragments occurred during anaphase, and that the cell cycle was delayed at G2/M, which led to the occurrence of endoreduplication. Further, a large number of DNA double-strand breaks (DSBs) occurred in thense1andnse3mutants, and the expression ofAtNSE1andAtNSE3was up-regulated following treatment of the plants with DSB inducer compounds, suggesting thatAtNSE1andAtNSE3have a role in DNA damage repair. Therefore, we conclude thatAtNSE1andAtNSE3facilitate DSB repair and contribute to maintaining genome stability and cell division in mitotic cells. Thus, we think thatAtNSE1andAtNSE3may be crucial factors for maintaining proper early embryonic and post-embryonic development.