We use atomic force microscopy (AFM) in conjunction with fluorescence relaxation dynamics to establish the relationship between the physical morphology and optical response of zirconium-phosphonate (ZP) monolayers containing oligothiophene chromophores. For ZP monolayers formed on SiOx, island structures are seen with AFM in the size range 40-100 Angstrom with the nearest neighbor island spacing varying from 80 to 200 Angstrom. For these same surfaces, the fluorescence population relaxation dynamics we measure are nonexponential, chromophore concentration-independent, and identical for two different chromophores. This finding is fully consistent with the AFM data, and the results can be understood using an excitation hopping model. The spectroscopic data are consistent with aggregated islands similar to 50-100 Angstrom in diameter. We demonstrate that the spectroscopic and physical domain sizes present on ZP/SiOx monolayers are the same. Studies using several initial priming schemes point to the silanol group distribution on the surface determining structural heterogeneity with intermolecular interactions between chromophores playing a secondary role.