The electromagnetic spectrum has been exploited for centuries by scientists and engineers to develop new technologies. The visible (VIS, 400-700 nm) and near infrared (NIR, 700-1000 nm) regions have been widely explored for photoactive materials. Beyond that lies the shortwave infrared (SWIR, 1000-2000 nm) region of the electromagnetic spectrum which has garnered interest for military purposes, quality assurance, telecommunications and diagnostics. Photoactive SWIR materials consists of carbon nanotubes, rare earth doped nanoparticles, quantum dots, conjugated polymers and small molecules. Of particular interest are polymethine fluorophores, which are one of the few classes of small molecules for the SWIR region, but development of these dyes that can absorb and emit within the SWIR region is still in its infancy. In this dissertation, long wavelength absorbing and emitting polymethine dyes are synthesized and studied to develop an understanding of structural modifications and their impact on photophysical properties. Chapter One is a perspective on the polymethine dye scaffold and its utility for the SWIR region. Chapter Two focuses on tuning a flavylium heptamethine dye scaffold through substituent identity to match excitation lasers to obtain real-time excitation multiplexing in vivo. In Chapter Three, we further modify the flavylium heptamethine scaffold by changing the substituent position in order to gain a better understanding of the effect of electron donors on the spectral properties. In Chapters Two and Three, we observed that small structural modifications gave small red shifts in λmax, thus in Chapter Four, we explored heteroatom exchange from oxygen to silicon in a xanthene based polymethine fluorophore to induce a red shift of 100 nm. In Chapter Five, further studies on the structural modification of the flavylium heptamethine scaffold at the 6-position and post-synthetic counterion exchange were explored to help improve excitation multiplexed imaging. Finally in Chapter Six, supramolecular methods were explored in the form of J-aggregation as a route to SWIR materials. Small structural modifications were made on a thiazole cyanine scaffold to examine their effect on aggregation properties. The fundamental understanding developed within those studies were applied back to the flavylium heptamethine scaffold to yield an aggregate with λmax,abs at 1350 nm.