Substituted thymines, where oxygen is replaced by sulfur or selenium, affect a variety of functions in biological systems and are prospective phototherapeutic agents. In this study, we show that an interplay between two types of delocalization, one due to conjugation and the other owing to the varying size of the substituted atom, leads to distinct absorption spectra and electrophilic sites in substituted thymines. This result is supported by ab initio quantum chemical calculations and a simple particle-in-a-box model. The model explains the unexpected variation in the absorption of 2-thiothymine and 4-thiothymine and makes an unanticipated prediction about the nature of the LUMO in 2-selenothymine that is confirmed by quantum chemical calculations. Here, delocalization due to the large size of selenium dominates that due to conjugation; in essence, a 2-center delocalization exerts a greater influence on molecular properties than a 4-center delocalization. The study highlights that the widely used concept of delocalization may be affected not only by the long-established idea of double bond conjugation but also delocalization owing to the size of atoms.