Because of their advantageous properties, fluorescent organic molecules have been used extensively in various applications. Despite the high demand for fluorophores, there are only a limited number of fluorescent organic core skeletons with sufficient flexibility in their synthetic strategies. The rational design of fluorescent probes having desirable photophysical properties is still far from being achieved because of the complexity of underlying photophysical phenomena of fluorescent small molecules. To study and improve the photophysical properties of fluorescent core skeletons, many efforts have been pursued. Traditionally, targeted approach had been used to rationally study the photophysical properties of known fluorescent core skeleton. On the other hand, recent studies showed that combinatorial approach can act as a powerful tool to discover or develop novel fluorescent probes. Through a comparison between targeted synthesis and combinatorial approach in the study of fluorescent organic compounds, we can conclude that the targeted synthesis with rational design and systematic modification using combinatorial approach are complementary to each other for the discovery of novel, small molecules with desired photophysical properties.