In the present work, we study and compare the structure and sensing properties of thin films of unsubstituted palladium phthalocyanine (PdPc) and hexadecafluorosubstituted palladium phthalocyanine (PdPcF16). Thin films of PdPc and PdPcF16 were obtained by the method of organic molecular beam deposition, and their structure was studied using UV-visible spectroscopy, X-ray diffraction, and atomic force microscopy techniques. The electrical sensor response of PdPc films toward ammonia and hydrogen was investigated and compared with that of PdPcF16 films. The nature of interaction between the phthalocyanines films and some gaseous analyte molecules has been clarified using quantum chemical (DFT) calculations. (Graph Presented).