The effects of different DNA molecules of the same length on the morphology of gold nanoparticles during synthesis are investigated. While spherical nanoparticles (AuNS) are observed in the presence of 30-mer poly T, like that in the absence of DNA, 30-mer poly A or poly C induces formation of the flower-shaped gold nanoparticle (AuNF). Detailed mechanistic studies indicate that the difference in DNA affinity to the AuNP plays a major role in the different morphology control processes. The DNA adsorbed on the AuNS surface could act as template to mediate the formation of flower-like gold nanoparticles. The formation of the AuNF can result from either selective deposition of the reduced gold metal on AuNS templated by surface bound DNA or uneven growth of the AuNS due to the binding of DNA to the surface. Furthermore, DNA functionalization with high stability was realized in situ during the one-step synthesis while retaining their biorecognition ability, allowing programmable assembly of new nanostructures. We have also shown that the DNA-functionalized nanoflowers can be readily uptaken by cells and visualized under dark-field microscopy.