Ternary two-dimensional dichalcogenide alloys exhibit compositionally modulated electronic structure, and hence, control of dopant concentration within each individual layer of these compounds provides a powerful tool to efficiently modify their physical and chemical properties. The main challenge arises when quantifying and locating the dopant atoms within each layer in order to better understand and fine-tune the desired properties. Here we report the synthesis of molybdenum disulfide substitutionally doped with a broad range of selenium concentrations, resulting in over 10% optical band gap modulations in atomic layers. Chemical analysis using Z-contrast imaging provides direct maps of the dopant atom distribution in individual MoS2 layers and hence a measure of the local optical band gaps. Furthermore, in a bilayer structure, the dopant distribution is imaged layer-by-layer. This work demonstrates that each layer in the bilayer system contains similar local Se concentrations, randomly distributed, providing new insights into the growth mechanism and alloying behavior in two-dimensional dichalcogenide atomic layers. The results show that growth of uniform, ternary, two-dimensional dichalcogenide alloy films with tunable electronic properties is feasible.