Edible films and coatings based on biopolymers to protect and extend the shelf life of food and medicine can be functionalized, by applying a holographic marker on the coating surface for marking products or sensing storage conditions. In this work, holographic markers were prepared on the surface of thin biopolymer coatings based on starch, gelatin, agar and also starch/gelatin and starch/agar blends by the nanoimprint method from a film-forming solution. The morphology of the surface of holographic markers using optical microscopy in reflection mode was examined, as well as the reasons for its formation using an analysis of the flow curves of film-forming solutions. It was found that the surface morphology of the marker strongly depends on the composition, consistency index of film-forming solution and miscibility of the components. It was shown that the starch/agar film-forming solution at the ratio of 70/30 wt.% has a low consistency index value of 21.38 Pa·s0.88, compared to 64.56 Pa·s0.67 for pure starch at a drying temperature of 30 °C, and the components are well compatible. Thus, an isotropic morphology of the holographic marker surface was formed and the value of diffraction efficiency of 3% was achieved, compared to 1.5% for the marker made of pure starch. Coatings without holographic markers were analyzed by tensile strength and water contact angle, and their properties are highly dependent on their composition.