Synthesis, isomerisation and structure elucidation of the title compounds 1-6 and its isomers 7-12 by FTIR, 1 H, 13 C, 15 N, 77 Se NMR spectroscopy is reported. Ethyl 2-(3-acylselenoureido)thiophene-3-carboxylates and their benzoanalogues (where acyl is benzoyl and pivaloyl) were prepared by addition of ethyl 2-aminothiophene-3-carboxylates and ethyl 2-aminobenzoate on benzoyl-or pivaloylisoselenocyanate in acetone solution. An isomerization of 1-6 to the corresponding 3-acylisoselenoureas 7-12 was obtained. The isomerisation proceeds either by irradiation with light (340-400 nm) or in the case of benzoylderivatives 1, 3, 5 by treatment with acetic acid. On the other hand the acid action in the pivaloyl set inhibited this isomerisation and evoked the retroisomerisation reaction of 8, 10, 12 to 2, 4, 6. Thermal analyses showed that isomerisation can be initiated also by heating. These changes proceed in the solid phase as an exothermic process at an elevated temperature but always below the temperature of melting. The structure 2 was supported by X-ray analysis. Molecular design of 2 and 8 was modeled during application of ab initio quantum chemistry calculation.