We have synthesized and characterized a library of near-infrared (NIR) heptamethine cyanine dyes for biomedical application as photoacoustic imaging and photothermal agents. These hydrophobic dyes were incorporated into a polymer-based nanoparticle system to provide aqueous solubility and protection of the photophysical properties of each dye scaffold. Among those heptamethine cyanine dyes analyzed, 13 compounds within the nontoxic polymeric nanoparticles have been selected to exemplify structural relationships in terms of photostability, photoacoustic imaging, and photothermal behavior within the NIR (∼650-850 nm) spectral region. The most contributing structural features observed in our dye design include hydrophobicity, rotatable bonds, heavy atom effects, and stability of the central cyclohexene ring within the dye core. The NIR agents developed within this project serve to elicit a structure-function relationship with emphasis on their photoacoustic and photothermal characteristics aiming at producing customizable NIR photoacoustic and photothermal tools for clinical use.