Here, we have prepared DNA-functionalized gold nanorods (Au NRs@HS-DNA) through a combination of stepwise ligand exchange, involving a sequential aqueous–organic–aqueous transfer, and subsequent oligonucleotide grafting. The as-prepared Au NRs@HS-DNA display a high and long-term colloidal stability in high ionic strength media, and they are proved very stable and biocompatible in cell culture media. We discuss important aspects in order to obtain a high DNA loading and to ensure colloidal stability during the functionalization process. We also demonstrate the high biocompatibility (>95% viability, low ROS activity, normal cell growth rate) of the DNA-functionalized Au NRs, which is mainly ascribed to the efficient removal of cetyltrimethylammonium bromide (CTAB) from their surface and to their high stability. These Au NR–DNA conjugates can be selectively addressed with a laser beam in a binary sample mixture comprising clusters of self-assembled DNA-functionalized spherical Au nanoparticles (NPs) and clusters of self-assembled DNA-functionalized Au NRs. We demonstrate that each colloidal cluster can be selectively disassembled by exciting the NPs close to their respective plasmon resonance maxima with microsecond laser pulses at 532 nm (for the spherical Au NPs) or 1064 nm (for the Au NRs). To the best of our knowledge this is the first report of an assay that allows optical induction of the selective DNA melting of different sequences within one solution, regardless of their respective melting temperatures. As a proof of concept, we demonstrate that the Au NR–DNA conjugates can be used as NIR-addressable probes and mediators for ultrafast and selective DNA melting and, in turn, for the selective detection of DNA.