The near infrared (NIR) region is known as the therapeutic window has gathered significant attention in biomedical research due to its potential for deep tissue imaging and therapeutic applications. Therefore, the development of NIR fluorophores remains an active and evolving area of study. This thesis introduces several NIR fluorophore scaffolds such as donor acceptor fluorophores, cyanine dyes with modified linker systems and hemicyanine dyes which can be used as potential bioimaging agents. First, the synthesis and characterization of novel donor acceptor fluorophores and their optical properties are presented. These fluorophores have shown cytotoxicity against triple negative breast cancer cell lines, and they are fluorescent in the NIR region therefore they can be used as potential theragnostic agents. Additionally, their interaction with bovine serum albumin and DNA has also been studied. Second, novel cyanine dyes were synthesized by structure inherent targeting approach by using two different linker units. The cyanine scaffold was modified with quaternary ammonium, difluoro and morpholine units. Several different modifications on the indole heterocycles have resulted with a large library of dyes. The quaternary ammonium linker containing dyes were further modified at the meso position to introduce triple positive charged cyanine dyes. These dyes have found application as unique cartilage targeting agents in the NIR II region. The dyes have shown bright and precise imaging of the targeted tissue with high signal to background ratio. Third, hemicyanine dyes were synthesized as potential optoacoustic agents in the NIR region. These dyes have a donor acceptor scaffold where xanthene unit is the donor moiety and various indole heterocycles are the acceptor units. Their physicochemical, optical and pH sensing properties were studied in buffer solution. Due to their low cytotoxicity and high optoacoustic signals, they are promising optoacoustic agents.