We experimentally evaluated the control of the mobility speed of organic chromophores in polydimethylsiloxane (PDMS) by developing novel chromophores with different molecular structures. As novel chromophores, PDMS-soluble coumarin- and pyrromethene-based chromophores were developed by attaching heptamethyltrisiloxane (HMTS). Then, the optical and mobility properties of these novel chromophores were evaluated. The investigation of mobility characteristics revealed that molecular weight and solubility both influence the diffusion coefficient. In the case of low solubility, molecular weight is the dominant factor in determining the diffusion coefficient. On the other hand, molecular solubility is the dominant factor at high solubility. To the best of our knowledge, this is the first investigation on controlling the diffusion coefficient in PDMS through the molecular weight and solubility.