Heterostructures of quaterthiophene and sexithiophene were grown by organic molecular beam deposition both on fused silica and on potassium acid phthalate (001) single crystals. The influence of both the substrate and the order of deposition on the sample morphology and, in turn, on their optical properties has been investigated. In particular, by changing the deposition conditions, the heterostructures have been found to grow either in an island or in a layer by layer mode. The emission spectra of the latter show the individual quaterthiophene and sexithiophene bands, while the spectra of the island samples are related to effects of the boundary between quaterthiophene and sexithiophene.