Argonaute (AGO) proteins are the core of the RNA-induced gene silencing complex which regulate a wide variety of processes in plants, from organ development to abiotic stress responses.  They have been identified in many plants, but little is known in longan (Dimocarpus longan Lour.), and how AGO functions in the signaling pathways in plant embryos in response to changing environmental stimuli remains unclear.  In the present research, a genome-wide analysis of the AGO gene family members and their roles in somatic embryogenesis (SE), zygotic embryogenesis (ZE), tissue developmental processes, and responses to hormones, light and abiotic stress in longan were conducted.  Ten longan AGO genes were identified genome-wide and divided into four clades.  They were distributed on chromosomes 1, 4, 8, 10, 12, 13, 14, and 15, and had 2–23 introns.  The expression profiling implied that DlAGOs regulated early and middle embryogenesis, as well as developmental processes of seed, flower, and stem in longan.  In addition, the transcript levels of DlAGOs in response to exogenous hormones, light and abiotic stress showed differences in expression patterns.  These results provide the useful information for further elucidation of RNAi-mediated gene silencing in longan embryogenic callus (EC).