The specific binding between aptamers and proteins has drawn much attention recently both in molecular biochemistry and sensing field since aptamers have the advantage of binding specificity and generality, so that the aptamer−protein recognition has now been developed as a model for biorecognition. The work presented herein illustrates a novel method for the end-to-end assembly of gold nanorods (AuNRs) based on the specific aptamer−protein recognition. Owing to the capping reagent of cetyltrimethylammonium bromide (CTAB) on the longitudinal side surface of AuNRs, the thiol-modified aptamer of thrombin preferentially binds onto the edges of AuNRs by the formation of a thiol−gold covalent bond. The addition of thrombin, which has two binding sites for its aptamer, initiated the end-to-end assembly of AuNRs, which could be confirmed with scanning electronic microscopic (SEM) imaging. The structures of the assembled AuNRs were determined by the concentrations of thrombin and the assembly procedures. All of t...