It is important to examine the deposition mechanism of crystalline carbon nitrides and to investigate the linkage between bio-molecular and superhard materials. Two different CN compound bio-molecular targets with the sixfold ring structure similar to that in the hypothetical beta -C3N4 were proposed to be used for synthesizing carbon nitride films on different substrates by reactive ion beam sputtering. Effect of the substrate material and the correlation between the bonding characters of the different target materials and the deposited films were examined. The deposited films exhibit no significant differences in the atomic NIC ratio and film properties at the condition of 1000 eV Ar-ion beam, no matter which one of the two target materials and which one of the seven substrate materials are. The XPS and AES analyses reveal that the atomic NIC ratio of the films can go up to 0.50, which is much higher than most of the reported values (0.2-0.35). The FTIR, XPS and Raman spectra clearly indicate the co-existence of chemical bondings of C-N single bond and C=N double bond; and no detectable C dropN triple bonding is observed, which forms a favor basis for further processing of the films to improve the film quality. The XRD, electron diffraction, TEM and AFM analyses indicate that the deposited films may consist of the nano-sized beta -C3N4 crystaflites embedded in matrix of graphite form of C3N4 Structure, and the volume concentrations of the crystalline phases are high enough to be detected by XRD. The implication of the results is that one highly probable way to explore the deposition mechanisms of crystalline carbon nitrides is to manipulate chemical bonding information using different target materials.