Although numerous studies have been conducted on the toxicity and biodistribution of AgNPs and corresponding ionic counterparts, it is still debatable whether the toxicity originates from the accumulation of particles within specific organs or is mediated by the dissolved Ag ions. To gain a better insight into the toxic mechanisms of AgNPs, two aggregation-induced emission fluorogens (AIEgens; AIEgens-coated AgNPs and a fluorogenic Ag+ sensor) were employed for the in situ visualization and quantitative analysis of distribution patterns of AIE-AgNPs and corresponding Ag ions in different organs of medaka larvae. The 96 h LC50 of AIEgens-coated AgNPs (AIE-AgNPs) was 10-20 mg/L, which was much higher than that of the citrate-coated AgNPs (Cit-AgNPs, 2.39-3.24 mg/L) and AgNO3 (0.23 mg/L), suggesting that the AIE-AgNPs were much more biocompability than Cit-AgNPs or AgNO3. The LC50 of AgNO3 was approximately 10% of the LC50 of Cit-AgNPs, which was comparable to the percentage of Ag+ released from Cit-AgNPs. The novel AIE method for the first time simultaneously analyzed the quantitative distribution patterns of AIE-AgNPs and corresponding Ag ions in different organs of medaka larvae. AIE-AgNPs and Ag ions showed distinct distribution patterns, in which AIE-AgNPs were concentrated in intestine and liver, accounting for 53.4% and 32.1% of the total AIE-AgNPs accumulated in medaka larvae, respectively. In contrast, Ag ions were accumulated mainly (92.5%) in the intestine of medaka larvae. The toxicity of AgNPs toward medaka larvae was attributed mainly to the released Ag ions which could potentially disrupt the absorptive capacity of the intestinal epithelium and induce digestive dysfunction. Our study provided a new technique for simultaneous monitoring of the AgNPs and corresponding Ag ions in the biological systems.