Histone acetylation and deacetylation are essential for chromatin modifications that regulate various cellular functions. This study identified nine histone deacetylase (HDAC) genes in the yellow fever mosquito, Aedes aegypti, and investigated their roles in female reproduction and embryonic development using RNA interference (RNAi). RNAi-mediated knockdown of HDAC1 (Histone deacetylase 1), HDAC3 (Histone deacetylase 3), HDAC4 (Histone deacetylase 4), and SIRT2 (Sirtuin 2) resulted in severe defects in oocyte development and reduced egg-laying compared with control insects injected with double-stranded RNA (dsRNA) targeting the green fluorescent protein gene (dsGFP). RT-qPCR analysis showed that vitellogenin and its receptor genes are downregulated, leading to suppressed oocyte maturation in mosquitoes injected with dsRNAs targeting HDAC1, HDAC3, HDAC4, and SIRT2 compared with controls. Furthermore, knockdown of HDAC3, HDAC6, and HDAC8 inhibited embryonic development, resulting in reduced hatch rates. These results suggest that HDACs play a vital role in reproduction and embryonic development in Ae. aegypti.