With utilization of a transparent medaka fish (Oryzias latipes) and fluorescent confocal microscopy, essential knowledge about biodistribution of fluorescein isothiocyanate (FITC)-functionalized mesoporous silica nanoparticles (MSNs) within a living organism becomes accessible without tissue dissection. Data evidences bioaccumulation of FITC-MSNs in liver, gill, and intestine after one month's aqueous exposure. FITC-MSNs were mainly retained in liver for at least a week even after those in intestine had been excreted out.