We present the study of electrochemical deposition of silver on highly oriented pyrolytic graphite from the aqueous solution containing 3-mercaptopropionic acid. The investigations were conducted by electrochemical methods and scanning tunneling microscopy. It was shown that the presence of 3-mercaptopropionic acid in the solution strongly influences the deposition process of Ag. The immediate adsorption of the thiol on the deposited metal results in formation of nanosized silver islands distributed on the graphite surface. These islands consist of sets of nanorods that are 3-8 nm in diameter and 50-250 nm in length.