This thesis reviews the history, known synthetic procedures and applications of semi-squaraine dyes, 1,2-squaraine dyes and 1,3-squaraine dyes in the first chapter. The second chapter outlines the synthesis, characterization, and photophysical data of oxycyclobutenolate dyes compared to dicyanomethylene functionalized squaraine dyes. The structure and purity of each compound were confirmed by 1H and 13C NMR and Mass spectrometry. Additionally, their photophysical properties and in vivo bio-distribution were studied after confirmation through characterizations. Dyes functionalized with the dicyanomethylene acceptor group displayed improved photostability and physicochemical properties over their oxycyclobutenolate counterparts. Furthermore, the biodistribution data revealed that dyes substituted with the trimethylammonium bromide group displayed improved lymph node and thyroid gland targeting.